From a639f0833c02e7fc6c7ad2cc8423f8074bcc37bd Mon Sep 17 00:00:00 2001
From: Commandre Benjamin <benjamin.commandre@irstea.fr>
Date: Thu, 29 Nov 2018 15:33:53 +0100
Subject: [PATCH] Nettoyage du code + Optimisation
---
PHYMOBAT.py | 540 ++++++++++++++++++++++++++------------------------
Processing.py | 400 +++++++++++++++++++------------------
Sample.py | 140 ++++++-------
Vector.py | 87 ++++----
4 files changed, 590 insertions(+), 577 deletions(-)
diff --git a/PHYMOBAT.py b/PHYMOBAT.py
index ca791f8..39dbf39 100644
--- a/PHYMOBAT.py
+++ b/PHYMOBAT.py
@@ -1,18 +1,18 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
-#
+#
# Copyright 2016 Sylvio Laventure (IRSTEA - UMR TETIS)
#
# PHYMOBAT 3.0 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
-#
+#
# PHYMOBAT 3.0 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
-#
+#
# You should have received a copy of the GNU General Public License
# along with PHYMOBAT 3.0. If not, see <http://www.gnu.org/licenses/>.
@@ -52,7 +52,7 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
"""
Interface main class. It makes to link ``ui_PHYMOBAT_tab`` and ``Processing``.
"""
-
+
def __init__(self, mode = Constantes.SIMPLE_MODE, parent=None):
super(PHYMOBAT, self).__init__(parent)
Processing.__init__(self)
@@ -65,8 +65,8 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.current_mode = mode
self.logger = Outils.Log("Log", "Phymobat")
-
- #Â To select interface's parameters
+
+ #Â To select interface's parameters
if self.current_mode == Constantes.EXPERT_MODE:
self.logger.info("Expert mode.")
global Ui_PHYMOBAT, _translate
@@ -75,16 +75,16 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.logger.info("Simple mode.")
global Ui_PHYMOBAT, _translate
from ui_PHYMOBATs_tab import Ui_PHYMOBAT, _translate
-
+
self.initUI()
-
+
def initUI(self):
-
+
"""
Get initial values from interface after a click button.
-
+
There is :
-
+
- Connect browser button to search a path
* Main folder path
* Study area shapefile path
@@ -94,15 +94,15 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
* Output classification shapefile path
* Sample shapefile path
* Image path for samples if the first processing image hasn't been launched
-
+
- Connect button to add sample in the memory list
- Connect button to clear sample record. Clear in the interface and in the memory list
- Connect close|ok button
- Connect menu bar tab (Open backup, save in a xml file, close, help, About PHYMOBAT, mode)
- Initialize backup variable
-
+
"""
-
+
#Â Initial interface
self.ui = Ui_PHYMOBAT()
self.ui.setupUi(self)
@@ -112,41 +112,41 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
#Â Main folder path
self.ui.lineEdit_principal_folder.clear()
self.ui.pushButton_browser_principal_folder.clicked.connect(self.f_path_folder_dpt)
-
+
# Block other function if SpotWorldHeritage is chose
try :
self.ui.comboBox_captor.currentIndexChanged.connect(self.block_for_swh)
except AttributeError:
pass
-
+
# VHRS image path
self.ui.lineEdit_VHRS.clear()
self.ui.pushButton_browser_VHRS.clicked.connect(self.f_path_ortho)
-
+
# Study area shapefile path
self.ui.lineEdit_area_path.clear()
self.ui.pushButton_browser_area_path.clicked.connect(self.f_path_area)
-
+
# Proxy
self.ui.proxy.clicked.connect(self.f_proxy)
-
+
#Â Segmentation shapefile path
self.ui.lineEdit_segmentation.clear()
self.ui.pushButton_browser_segmentation.clicked.connect(self.f_path_segm)
-
+
#Â MNT image path
self.ui.lineEdit_MNT.clear()
self.ui.pushButton_browser_MNT.clicked.connect(self.f_path_mnt)
-
+
# Output classification shapefile path
self.ui.lineEdit_output.clear()
self.ui.pushButton_browser_output.clicked.connect(self.f_output_name_moba)
-
+
# Sample shapefile path.
# For the simply mode, RPG file sample.
self.ui.lineEdit_sample_path.clear()
self.ui.pushButton_browser_sample_path.clicked.connect(self.enter_sample_name)
-
+
if self.current_mode == Constantes.SIMPLE_MODE:
# For the simply mode, grass/wooden file sample.
self.ui.lineEdit_sample_path_2.clear()
@@ -154,7 +154,7 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
# For the simply mode, wooden file sample.
self.ui.lineEdit_sample_path_3.clear()
self.ui.pushButton_browser_sample_path_3.clicked.connect(self.enter_sample_name_ll)
-
+
#Â Image path for samples if the first processing image hasn't been launched
try:
self.ui.pushButton_img_sample.clicked.connect(self.img_sample_name)
@@ -167,18 +167,18 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.ui.pushButton_add_sample.clicked.connect(self.add_sample)
except AttributeError:
pass # Simple mode
-
+
# Connect button to clear sample record. Clear in the interface and in the memory list
try:
self.ui.pushButton_clear_sample.clicked.connect(self.clear_sample)
except AttributeError:
pass # Simple mode
-
+
#Â Connect close|ok button
# self.ui.buttonBox.button(QtWidgets.QDialogButtonBox.Close).clicked.connect(self.close_button)
self.ui.buttonBox.button(QtWidgets.QDialogButtonBox.Close).clicked.connect(self.close_button)
self.ui.buttonBox.button(QtWidgets.QDialogButtonBox.Ok).clicked.connect(self.ok_button)
-
+
#Â Connect Menu bar
self.ui.actionOuvrir.triggered.connect(self.open_backup) # Open backup
self.ui.actionSauver.triggered.connect(self.save_backup) #Â Save field name on the interface
@@ -187,31 +187,31 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.ui.actionA_propos_de_PHYMOBAT.triggered.connect(self.about_PHYMOBA) # About PHYMOBA
self.ui.actionMode_Simplifi.triggered.connect(lambda checked, mode=Constantes.SIMPLE_MODE: self.change_mode(mode)) # To open the simple apply
self.ui.actionMode_expert.triggered.connect(lambda checked, mode=Constantes.EXPERT_MODE: self.change_mode(mode)) # To open the expert apply
-
+
self.rpg_tchek = [] #Â To backup rpg mode
self.img_sample = [] # To backup
-
+
#Â Connect change line edit on sample path to extract fieldnames. For the simply mode, this
# is with RPG sample
self.ui.lineEdit_select_sample_fieldname_1.textChanged.connect(self.field_display_1)
self.ui.lineEdit_select_sample_fieldname_2.textChanged.connect(self.field_display_2)
-
+
# To choose the classification method
if self.current_mode == Constantes.EXPERT_MODE:
if self.ui.radioButton_rf.isChecked():
self.ui.checkBox_classifier_1.setEnabled(False)
self.ui.checkBox_classifier_2.setEnabled(False)
-
- self.ui.radioButton_rf.toggled.connect(self.activate_level)
+
+ self.ui.radioButton_rf.toggled.connect(self.activate_level)
self.ui.radioButton_s.toggled.connect(self.activate_level)
-
+
if self.current_mode == Constantes.SIMPLE_MODE:
#Â Connect change line edit to grass/wooden sample
self.ui.lineEdit_select_sample_fieldname_3.textChanged.connect(self.field_display_3)
self.ui.lineEdit_select_sample_fieldname_4.textChanged.connect(self.field_display_4)
self.ui.lineEdit_select_sample_fieldname_5.textChanged.connect(self.field_display_5)
self.ui.lineEdit_select_sample_fieldname_6.textChanged.connect(self.field_display_6)
-
+
#Â Change connect for classification checkboxes
try:
self.ui.checkBox_classifier_1.stateChanged.connect(self.display_one_level)
@@ -219,11 +219,11 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.ui.checkBox_classifier_3.stateChanged.connect(self.display_all_levels)
except AttributeError:
pass # Simple mode
-
- def get_variable(self):
+
+ def get_variable(self):
"""
Add a all system value like :
-
+
- Main folder path by line edit
- Satellite captor name by combo box
- Classification year by line edit
@@ -234,77 +234,77 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
- Segmentation shapefile path path by line edit
- Output classification shapefile path by line edit
- Output shapefile field name by line edit and field type by combo box
-
+
"""
#Â Main folder path by line edit.
self.path_folder_dpt = "%s" % self.ui.lineEdit_principal_folder.text()
-
+
# Satellite captor name by combo box
try:
self.captor_project = self.ui.comboBox_captor.currentText()
except AttributeError:
self.captor_project = "Landsat"
-
+
# Classification year by line edit
self.classif_year = "%s" % self.ui.lineEdit_year_images.text()
-
+
# Study area shapefile path by line edit
self.path_area = "%s" % self.ui.lineEdit_area_path.text()
-
+
#Â Connexion username and password by line edit
self.user = "%s" % self.ui.lineEdit_user.text()
self.password = "%s" % self.ui.lineEdit_password.text()
-
+
#Â VHRS image path by line edit
self.path_ortho = "%s" % self.ui.lineEdit_VHRS.text()
-
+
#Â MNT image path by line edit
- self.path_mnt = self.ui.lineEdit_MNT.text()
-
+ self.path_mnt = self.ui.lineEdit_MNT.text()
+
#Â Output shapefile field name by line edit and field type by combo box
try:
if self.ui.checkBox_classifier_1.isChecked() and self.ui.lineEdit_fieldname_1.text() != '':
self.out_fieldname_carto.append("%s" % self.ui.lineEdit_fieldname_1.text())
self.out_fieldtype_carto.append(eval("ogr.OFT%s" % self.ui.comboBox_fieldname_1.currentText()))
-
+
if self.ui.checkBox_classifier_2.isChecked() and self.ui.lineEdit_fieldname_12.text() != '':
self.out_fieldname_carto.append("%s" % self.ui.lineEdit_fieldname_12.text())
self.out_fieldtype_carto.append(eval("ogr.OFT%s" % self.ui.comboBox_fieldname_12.currentText()))
-
+
if self.ui.lineEdit_fieldname_2.text() != '':
self.out_fieldname_carto.append("%s" % self.ui.lineEdit_fieldname_2.text())
self.out_fieldtype_carto.append(eval("ogr.OFT%s" % self.ui.comboBox_fieldname_2.currentText()))
-
+
if self.ui.checkBox_classifier_3.isChecked() and self.ui.lineEdit_fieldname_13.text() != '':
self.out_fieldname_carto.append("%s" % self.ui.lineEdit_fieldname_13.text())
self.out_fieldtype_carto.append(eval("ogr.OFT%s" % self.ui.comboBox_fieldname_13.currentText()))
-
+
if self.ui.lineEdit_fieldname_23.text() != '':
self.out_fieldname_carto.append("%s" % self.ui.lineEdit_fieldname_23.text())
self.out_fieldtype_carto.append(eval("ogr.OFT%s" % self.ui.comboBox_fieldname_23.currentText()))
-
- if self.ui.lineEdit_fieldname_3.text() != '':
+
+ if self.ui.lineEdit_fieldname_3.text() != '':
self.out_fieldname_carto.append("%s" % self.ui.lineEdit_fieldname_3.text())
self.out_fieldtype_carto.append(eval("ogr.OFT%s" % self.ui.comboBox_fieldname_3.currentText()))
-
- if self.ui.lineEdit_fieldname_4.text() != '':
+
+ if self.ui.lineEdit_fieldname_4.text() != '':
self.out_fieldname_carto.append("%s" % self.ui.lineEdit_fieldname_4.text())
self.out_fieldtype_carto.append(eval("ogr.OFT%s" % self.ui.comboBox_fieldname_4.currentText()))
except AttributeError:
modes_fieldname = ["NIVEAU_1", "NIVEAU_2", "NIVEAU_3", "POURC"]
modes_fieldtype = [eval("ogr.OFTString"), eval("ogr.OFTString"), eval("ogr.OFTString"), eval("ogr.OFTReal")]
-
+
for mf in range(len(modes_fieldname)):
-
+
self.out_fieldname_carto.append(modes_fieldname[mf])
self.out_fieldtype_carto.append(modes_fieldtype[mf])
-
+
# Segmentation shapefile path path by line edit
self.path_segm = "%s" % self.ui.lineEdit_segmentation.text()
-
+
#Â Output shapefile field name by line edit and field type by combo box
self.output_name_moba = "%s" % self.ui.lineEdit_output.text()
-
+
def set_variable(self):
"""
Print number of available image from Theia's GeoJSON .
@@ -315,14 +315,14 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.ui.label_listing.setText(str(self.nb_avalaible_images))
except AttributeError:
pass # Simple mode
-
+
def f_path_folder_dpt(self):
"""
Open a input browser box to select the main folder path by line edit.
"""
infoldername = QtWidgets.QFileDialog.getExistingDirectory(self, "Principal folder path", os.getcwd(), QtWidgets.QFileDialog.ShowDirsOnly)
self.ui.lineEdit_principal_folder.setText(str(infoldername).replace('[','').replace(']','').replace(' ',''))
-
+
def block_for_swh(self):
"""
Function to block others function when SportWorldHeritage is selected in the comboxbox captor.
@@ -349,43 +349,43 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.ui.pushButton_browser_VHRS.setEnabled(True)
self.ui.tabWidget.setTabEnabled(1, True)
self.ui.tabWidget.setTabEnabled(2, True)
-
+
def f_path_ortho(self):
"""
Open a input browser box to select the VHRS image path by line edit.
"""
orthofilename = QtWidgets.QFileDialog.getOpenFileName(self, "THRS image", self.ui.lineEdit_principal_folder.text(), '*.TIF *.tif')[0]
- self.ui.lineEdit_VHRS.setText(str(orthofilename).replace('[','').replace(']','').replace(' ',''))
-
+ self.ui.lineEdit_VHRS.setText(str(orthofilename).replace('[','').replace(']','').replace(' ',''))
+
def f_path_mnt(self):
"""
Open a input browser box to select the MNT image path by line edit.
"""
mntfilename = QtWidgets.QFileDialog.getOpenFileName(self, "MNT image", self.ui.lineEdit_principal_folder.text(), '*.TIF *.tif')[0]
- self.ui.lineEdit_MNT.setText(str(mntfilename).replace('[','').replace(']','').replace(' ',''))
-
+ self.ui.lineEdit_MNT.setText(str(mntfilename).replace('[','').replace(']','').replace(' ',''))
+
def f_path_area(self):
"""
Open a input browser box to select the study area shapefile path by line edit.
- """
+ """
areafilename = QtWidgets.QFileDialog.getOpenFileName(self, "Area shapefile", self.ui.lineEdit_principal_folder.text(), '*.shp')[0]
self.ui.lineEdit_area_path.setText(str(areafilename).replace('[','').replace(']','').replace(' ',''))
-
- def f_proxy(self):
+
+ def f_proxy(self):
"""
Function to open a popup in order to enter proxy ID
- """
+ """
if self.w_proxy is None:
self.w_proxy = Popup.proxy_window()
self.w_proxy.show()
-
+
def f_path_segm(self):
"""
Open a input browser box to select segmentation shapefile path path by line edit.
"""
segmfilename = QtWidgets.QFileDialog.getOpenFileName(self, "Segmentation shapefile", self.ui.lineEdit_principal_folder.text(), '*.shp')[0]
self.ui.lineEdit_segmentation.setText(str(segmfilename).replace('[','').replace(']','').replace(' ',''))
-
+
def f_output_name_moba(self):
"""
Set the output classification shapefile path by line edit.
@@ -395,7 +395,7 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
if outfilename[-4:] != '.shp':
outfilename = outfilename + '.shp'
self.ui.lineEdit_output.setText(outfilename)
-
+
def enter_sample_name(self):
"""
Open a input browser box to select the sample shapefile path by line edit. With :func:`add_sample` conditions for the expert mode.
@@ -403,35 +403,35 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
"""
samplefilename = QtWidgets.QFileDialog.getOpenFileName(self, "Sample shapefile", self.ui.lineEdit_principal_folder.text(), '*.shp')[0]
self.ui.lineEdit_sample_path.setText(str(samplefilename).replace('[','').replace(']','').replace(' ',''))
-
+
def enter_sample_name_hl(self):
"""
- Open a input browser box to select the grass and wooden sample shapefile path by line edit. With :func:`add_sample` conditions
+ Open a input browser box to select the grass and wooden sample shapefile path by line edit. With :func:`add_sample` conditions
for the simply mode.
"""
samplefilename_hl = QtWidgets.QFileDialog.getOpenFileName(self, "Grass/Wooden sample shapefile", self.ui.lineEdit_principal_folder.text(), '*.shp')[0]
self.ui.lineEdit_sample_path_2.setText(str(samplefilename_hl).replace('[','').replace(']','').replace(' ',''))
-
+
def enter_sample_name_ll(self):
"""
Open a input browser box to select the wooden sample shapefile path by line edit. With :func:`add_sample` conditions for the simply mode.
"""
samplefilename_ll = QtWidgets.QFileDialog.getOpenFileName(self, "Wooden sample shapefile", self.ui.lineEdit_principal_folder.text(), '*.shp')[0]
self.ui.lineEdit_sample_path_3.setText(str(samplefilename_ll).replace('[','').replace(']','').replace(' ',''))
-
+
def img_sample_name(self):
"""
Open a input browser box to select the image for samples path by line edit. With :func:`add_sample` conditions.
"""
imgsamplefilename = QtWidgets.QFileDialog.getOpenFileName(self, "Sample image", self.ui.lineEdit_principal_folder.text(), '*.TIF')[0]
self.ui.lineEdit_img_sample.setText(str(imgsamplefilename).replace('[','').replace(']','').replace(' ',''))
-
+
def add_sample(self):
"""
Add sample information and location to compute optimal threshold :
-
+
For the expert mode (mode=1) :
-
+
- Append a sample name by line Edit. *This is a check box* ``RPG``, *if the sample is RPG file. It launch the Rpg class. And append a other sample from Rpg class*.
- Append two existent sample field names by combobox. It will be the same.
- Append sample class names by line edit. One or more for every sample.
@@ -440,14 +440,14 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
- *This check box* ``Image echantillonee``, *image path for samples if the first processing image hasn't been launched*.
.. note:: This is for a image with one spectral band
- Clear all widget field at the end.
-
+
For the simply mode (mode=0):
-
+
- Append a sample name by a different line Edit (a line Edit for each sample).
- Append sample class names, existing sample fields and number of polygons (a different line Edit for each sample)
"""
-
- nb_sample = len(self.sample_name)#Â Compute number of samples added. Condition : max three.
+
+ nb_sample = len(self.sample_name)#Â Compute number of samples added. Condition : max three.
# Study area shapefile path by line edit if no processing other
# Because the function "Vector" need study area
@@ -455,24 +455,24 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
if not self.path_area :
self.forget_study_area()
-
+
if self.current_mode == Constantes.EXPERT_MODE:
# Expert mode
if nb_sample < 3 and not self.ui.lineEdit_sample_path.text().isEmpty() and \
not self.ui.lineEdit_select_sample_fieldname_1.text().isEmpty() and not self.ui.lineEdit_select_sample_fieldname_2.text().isEmpty() and \
not self.ui.lineEdit_select_sample_class_1.text().isEmpty() and not self.ui.lineEdit_select_sample_class_2.text().isEmpty() and \
not self.ui.lineEdit_select_sample_nb_poly.text().isEmpty() and not self.ui.lineEdit_area_path.text().isEmpty():
-
+
# Append a sample name by line Edit.
if self.ui.checkBox_RPG.isChecked():
- # Check box, if the sample of the RPG file. It launch the Rpg class. And append a other sample from Rpg class
+ # Check box, if the sample of the RPG file. It launch the Rpg class. And append a other sample from Rpg class
self.sample_name.append(self.i_rpg("%s" % self.ui.lineEdit_sample_path.text()))
self.rpg_tchek.append(1) # To backup
self.ui.checkBox_RPG.setChecked(False)
else:
self.sample_name.append("%s" % self.ui.lineEdit_sample_path.text())
self.rpg_tchek.append(0)
-
+
#Â Append two sample field names by line edit. It must be the same.
self.fieldname_args.append("%s" % self.ui.lineEdit_select_sample_fieldname_1.text())
self.fieldname_args.append("%s" % self.ui.lineEdit_select_sample_fieldname_2.text())
@@ -481,7 +481,7 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.class_args.append("%s" % self.ui.lineEdit_select_sample_class_2.text())
# Append number of polygons for every samples by line edit.
self.list_nb_sample.append("%s" % self.ui.lineEdit_select_sample_nb_poly.text())
-
+
nb_sample = len(self.sample_name) # Number of samples added
#Â Print in a plain text edit : sample name, two sample field names, sample class names and number of polygons.
cursor = self.ui.plainTextEdit_sample.textCursor()
@@ -497,7 +497,7 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
cursor.movePosition(QTextCursor.Down, QTextCursor.MoveAnchor)
self.ui.plainTextEdit_sample.setTextCursor(cursor)
self.ui.plainTextEdit_sample.insertPlainText(str(self.list_nb_sample[nb_sample-1]) + "\n")
-
+
#Â Check box, image path for samples if the first processing image hasn't been launched
# Warming : This is for a image with one spectral band
if self.ui.checkBox_img_sample.isChecked():
@@ -508,7 +508,7 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.img_sample.append(1)
else: #Â To backup
self.img_sample.append(0)
-
+
#Â Clear all line edit after addition, ie after click add button.
self.ui.lineEdit_sample_path.clear()
self.ui.lineEdit_select_sample_fieldname_1.clear()
@@ -516,14 +516,14 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.ui.lineEdit_select_sample_class_1.clear()
self.ui.lineEdit_select_sample_class_2.clear()
self.ui.lineEdit_select_sample_nb_poly.clear()
-
+
elif self.current_mode == Constantes.SIMPLE_MODE:
# Simple mode
# Append a sample name by line Edit.
- # For the sample of the RPG file. It launch the Rpg class. And append a other sample from Rpg class
+ # For the sample of the RPG file. It launch the Rpg class. And append a other sample from Rpg class
self.sample_name.append(self.i_rpg(self.ui.lineEdit_sample_path.text()))
-
+
#Â Append two sample field names by line edit. It must be the same.
self.fieldname_args.append(self.ui.lineEdit_select_sample_fieldname_1.text())
self.fieldname_args.append(self.ui.lineEdit_select_sample_fieldname_2.text())
@@ -534,7 +534,7 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
# Append number of polygons for every samples by line edit.
self.list_nb_sample.append(self.ui.lineEdit_select_sample_nb_poly.text())
-
+
# Same process that the RPG process except the start of the RPG class.
# To Grass/wooden
self.sample_name.append(self.ui.lineEdit_sample_path_2.text())
@@ -543,7 +543,7 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.class_args.append(self.ui.lineEdit_select_sample_class_3.text())
self.class_args.append(self.ui.lineEdit_select_sample_class_4.text())
self.list_nb_sample.append(self.ui.lineEdit_select_sample_nb_poly_2.text())
-
+
# To wooden
self.sample_name.append(self.ui.lineEdit_sample_path_3.text())
self.fieldname_args.append(self.ui.lineEdit_select_sample_fieldname_5.text())
@@ -551,7 +551,7 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.class_args.append(self.ui.lineEdit_select_sample_class_5.text())
self.class_args.append(self.ui.lineEdit_select_sample_class_6.text())
self.list_nb_sample.append(self.ui.lineEdit_select_sample_nb_poly_3.text())
-
+
def clear_sample(self):
"""
Function to clear sample record. Clear in the interface and in the memory list.
@@ -562,7 +562,7 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.list_nb_sample = []
self.rpg_tchek = []
self.img_sample = []
-
+
self.ui.lineEdit_sample_path.clear()
self.ui.lineEdit_select_sample_fieldname_1.clear()
self.ui.lineEdit_select_sample_fieldname_2.clear()
@@ -578,46 +578,46 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.ui.plainTextEdit_sample.insertPlainText("3 - Lingeux mixtes / denses\n")
self.ui.plainTextEdit_sample.insertPlainText("\n")
self.ui.plainTextEdit_sample.insertPlainText("\n")
- self.ui.plainTextEdit_sample.insertPlainText("")
-
+ self.ui.plainTextEdit_sample.insertPlainText("")
+
def field_display_1(self):
"""
Function to display fieldname class 1 in the other fieldname class 2 when text changed.
For the simply mode, this is RPG sample.
"""
self.ui.lineEdit_select_sample_fieldname_2.setText("%s" % self.ui.lineEdit_select_sample_fieldname_1.text())
-
+
def field_display_2(self):
"""
Function to display fieldname class 2 in the other fieldname class 2 when text changed.
For the simply mode, this is RPG sample.
"""
- self.ui.lineEdit_select_sample_fieldname_1.setText("%s" % self.ui.lineEdit_select_sample_fieldname_2.text())
-
+ self.ui.lineEdit_select_sample_fieldname_1.setText("%s" % self.ui.lineEdit_select_sample_fieldname_2.text())
+
def field_display_3(self):
"""
For the grass/wooden sample, a function to display fieldname class 1 in the other fieldname class 2 when text changed.
"""
self.ui.lineEdit_select_sample_fieldname_4.setText("%s" % self.ui.lineEdit_select_sample_fieldname_3.text())
-
+
def field_display_4(self):
"""
For the grass/wooden sample, a function to display fieldname class 2 in the other fieldname class 2 when text changed.
"""
- self.ui.lineEdit_select_sample_fieldname_3.setText("%s" % self.ui.lineEdit_select_sample_fieldname_4.text())
-
+ self.ui.lineEdit_select_sample_fieldname_3.setText("%s" % self.ui.lineEdit_select_sample_fieldname_4.text())
+
def field_display_5(self):
"""
For the wooden sample, a function to display fieldname class 1 in the other fieldname class 2 when text changed.
"""
self.ui.lineEdit_select_sample_fieldname_6.setText("%s" % self.ui.lineEdit_select_sample_fieldname_5.text())
-
+
def field_display_6(self):
"""
For the wooden sample, a function to display fieldname class 2 in the other fieldname class 2 when text changed.
"""
- self.ui.lineEdit_select_sample_fieldname_5.setText("%s" % self.ui.lineEdit_select_sample_fieldname_6.text())
-
+ self.ui.lineEdit_select_sample_fieldname_5.setText("%s" % self.ui.lineEdit_select_sample_fieldname_6.text())
+
def activate_level(self):
"""
To activate the first levels with seath method. This is in pushing on the decision tree radio button.
@@ -630,17 +630,17 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.ui.checkBox_classifier_1.setEnabled(False)
self.ui.checkBox_classifier_2.setEnabled(False)
self.ui.checkBox_classifier_3.setChecked(True)
-
+
def display_one_level(self):
"""
Function to display fieldnames option to classifier one level
"""
if self.ui.checkBox_classifier_1.isChecked():
-
+
# Don't checked others checkboxes
self.ui.checkBox_classifier_2.setChecked(False)
self.ui.checkBox_classifier_3.setChecked(False)
-
+
#Â Display options filednames
self.ui.label_chps_1 = QtWidgets.QLabel(self.ui.tab_3)
self.ui.label_chps_1.setObjectName("label_chps_1")
@@ -657,36 +657,36 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.ui.comboBox_fieldname_1 = QtWidgets.QComboBox(self.ui.tab_3)
self.ui.comboBox_fieldname_1.setObjectName("comboBox_fieldname_1")
self.ui.gridLayout_2.addWidget(self.ui.comboBox_fieldname_1, 11, 3, 1, 1)
-
+
self.ui.lineEdit_fieldname_1.setText(_translate("PHYMOBAT", "NIVEAU_1", None))
self.ui.comboBox_fieldname_1.addItem("String")
self.ui.comboBox_fieldname_1.addItem("Real")
-
+
self.ui.label_chps_1.setText(_translate("PHYMOBAT", " Champs\n"+" des entités", None))
- self.ui.label_chps_name_1.setText(_translate("PHYMOBAT", "Nom :", None))
- self.ui.label_chps_type_1.setText(_translate("PHYMOBAT", "Type :", None))
-
- if not self.ui.checkBox_classifier_1.isChecked():
+ self.ui.label_chps_name_1.setText(_translate("PHYMOBAT", "Nom :", None))
+ self.ui.label_chps_type_1.setText(_translate("PHYMOBAT", "Type :", None))
+
+ if not self.ui.checkBox_classifier_1.isChecked():
#Â Clear options filednames
try:
self.ui.label_chps_1.deleteLater()
self.ui.label_chps_name_1.deleteLater()
- self.ui.label_chps_type_1.deleteLater()
+ self.ui.label_chps_type_1.deleteLater()
self.ui.lineEdit_fieldname_1.deleteLater()
self.ui.comboBox_fieldname_1.deleteLater()
- except AttributeError:
+ except AttributeError:
pass
-
+
def display_two_levels(self):
"""
Function to display fieldnames option to classifier two first levels
"""
if self.ui.checkBox_classifier_2.isChecked():
-
+
# Don't checked others checkboxes
self.ui.checkBox_classifier_1.setChecked(False)
self.ui.checkBox_classifier_3.setChecked(False)
-
+
self.ui.label_chps_2 = QtWidgets.QLabel(self.ui.tab_3)
self.ui.label_chps_2.setObjectName("label_chps_2")
self.ui.gridLayout_2.addWidget(self.ui.label_chps_2, 13, 0, 2, 2)
@@ -695,7 +695,7 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.ui.gridLayout_2.addWidget(self.ui.lineEdit_fieldname_12, 13, 3, 1, 1)
self.ui.lineEdit_fieldname_2 = QtWidgets.QLineEdit(self.ui.tab_3)
self.ui.lineEdit_fieldname_2.setObjectName("lineEdit_fieldname_2")
- self.ui.gridLayout_2.addWidget(self.ui.lineEdit_fieldname_2, 13, 4, 1, 1)
+ self.ui.gridLayout_2.addWidget(self.ui.lineEdit_fieldname_2, 13, 4, 1, 1)
self.ui.label_chps_type_2 = QtWidgets.QLabel(self.ui.tab_3)
self.ui.label_chps_type_2.setObjectName("label_chps_type_2")
self.ui.gridLayout_2.addWidget(self.ui.label_chps_type_2, 14, 2, 1, 1)
@@ -708,46 +708,44 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.ui.label_chps_name_2 = QtWidgets.QLabel(self.ui.tab_3)
self.ui.label_chps_name_2.setObjectName("label_chps_name_2")
self.ui.gridLayout_2.addWidget(self.ui.label_chps_name_2, 13, 2, 1, 1)
-
+
self.ui.lineEdit_fieldname_12.setText(_translate("PHYMOBAT", "NIVEAU_1", None))
self.ui.comboBox_fieldname_12.addItem("String")
self.ui.comboBox_fieldname_12.addItem("Real")
self.ui.lineEdit_fieldname_2.setText(_translate("PHYMOBAT", "NIVEAU_2", None))
self.ui.comboBox_fieldname_2.addItem("String")
self.ui.comboBox_fieldname_2.addItem("Real")
-
+
self.ui.label_chps_type_2.setText(_translate("PHYMOBAT", "Type :", None))
self.ui.label_chps_2.setText(_translate("PHYMOBAT", " Champs\n"+" des entités", None))
self.ui.label_chps_name_2.setText(_translate("PHYMOBAT", "Nom :", None))
-
- if not self.ui.checkBox_classifier_2.isChecked():
+
+ if not self.ui.checkBox_classifier_2.isChecked():
#Â Clear options filednames
try:
self.ui.label_chps_2.deleteLater()
self.ui.label_chps_name_2.deleteLater()
- self.ui.label_chps_type_2.deleteLater()
+ self.ui.label_chps_type_2.deleteLater()
self.ui.lineEdit_fieldname_12.deleteLater()
self.ui.comboBox_fieldname_12.deleteLater()
self.ui.lineEdit_fieldname_2.deleteLater()
self.ui.comboBox_fieldname_2.deleteLater()
- except AttributeError:
+ except AttributeError:
pass
-
+
def display_all_levels(self):
"""
Function to display fieldnames option to launch complete classification
"""
-
if self.ui.checkBox_classifier_3.isChecked():
-
+
# Don't checked others checkboxes
self.ui.checkBox_classifier_1.setChecked(False)
self.ui.checkBox_classifier_2.setChecked(False)
-
self.ui.label_chps_name_3 = QtWidgets.QLabel(self.ui.tab_3)
self.ui.label_chps_name_3.setObjectName("label_chps_name_3")
self.ui.gridLayout_2.addWidget(self.ui.label_chps_name_3, 16, 2, 1, 1)
- self.ui.label_chps_3 = QtWidgets.QLabel(self.ui.tab_3)
+ self.ui.label_chps_3 = QtWidgets.QLabel(self.ui.tab_3)
self.ui.label_chps_3.setObjectName("label_chps_3")
self.ui.gridLayout_2.addWidget(self.ui.label_chps_3, 16, 0, 2, 2)
self.ui.label_chps_type_3 = QtWidgets.QLabel(self.ui.tab_3)
@@ -777,7 +775,6 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.ui.comboBox_fieldname_4 = QtWidgets.QComboBox(self.ui.tab_3)
self.ui.comboBox_fieldname_4.setObjectName("comboBox_fieldname_4")
self.ui.gridLayout_2.addWidget(self.ui.comboBox_fieldname_4, 17, 6, 1, 1)
-
self.ui.lineEdit_fieldname_13.setText(_translate("PHYMOBAT", "NIVEAU_1", None))
self.ui.comboBox_fieldname_13.addItem("String")
self.ui.comboBox_fieldname_13.addItem("Real")
@@ -788,19 +785,19 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.ui.comboBox_fieldname_3.addItem("String")
self.ui.comboBox_fieldname_3.addItem("Real")
self.ui.lineEdit_fieldname_4.setText(_translate("PHYMOBAT", "POURC", None))
- self.ui.comboBox_fieldname_4.addItem("Real")
+ self.ui.comboBox_fieldname_4.addItem("Real")
self.ui.comboBox_fieldname_4.addItem("String")
-
+
self.ui.label_chps_3.setText(_translate("PHYMOBAT", " Champs\n"+" des entités", None))
self.ui.label_chps_type_3.setText(_translate("PHYMOBAT", "Type :", None))
self.ui.label_chps_name_3.setText(_translate("PHYMOBAT", "Nom :", None))
-
- if not self.ui.checkBox_classifier_3.isChecked():
+
+ if not self.ui.checkBox_classifier_3.isChecked():
#Â Clear options filednames
try:
self.ui.label_chps_3.deleteLater()
self.ui.label_chps_name_3.deleteLater()
- self.ui.label_chps_type_3.deleteLater()
+ self.ui.label_chps_type_3.deleteLater()
self.ui.lineEdit_fieldname_13.deleteLater()
self.ui.comboBox_fieldname_13.deleteLater()
self.ui.lineEdit_fieldname_23.deleteLater()
@@ -809,13 +806,13 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.ui.comboBox_fieldname_3.deleteLater()
self.ui.lineEdit_fieldname_4.deleteLater()
self.ui.comboBox_fieldname_4.deleteLater()
- except AttributeError:
+ except AttributeError:
pass
-
+
def ok_button(self):
"""
Function to launch the processing. This function take account :
-
+
- The ``Multi-processing`` check box if the processing has launched with multi process.
By default, this is checked. It need a computer with minimum 12Go memory.
- Append a few system value with :func:`get_variable`.
@@ -826,127 +823,144 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
- to compute slope raster
- for classification processing.
"""
-
# Start the processus
startTime = time.time()
-
+
#Â To know if the processing must be launch on several thread
- self.mp = Constantes.MULTIPROCESSING_ENABLE if self.ui.checkBox_multiprocess.isChecked() else Constantes.MULTIPROCESSING_DISABLE
-
+ self.mp = Constantes.MULTIPROCESSING_ENABLE if self.ui.checkBox_multiprocess.isChecked() else Constantes.MULTIPROCESSING_DISABLE
+
self.get_variable() # Append a few system value
vs = 0 # Variable to launch VHRS texture processing
- dd = 0 # Variable to launch image downloading
+ dd = 0 # Variable to launch image downloading
ok = 1 #Â Variable to verify informations -> 0 not ok, 1 ok
-
+
if self.current_mode == Constantes.EXPERT_MODE:
#Â if download check box is checked only
- if not self.ui.checkBox_listing.isChecked() and self.ui.checkBox_download.isChecked():
+ if not self.ui.checkBox_listing.isChecked() and self.ui.checkBox_download.isChecked():
self.ui.checkBox_listing.setChecked(True)
-
- if ok == 1:
- # Compute a output slope raster
+
+ if ok == 1 :
+ # Compute a output slope raster
if self.ui.checkBox_MNT.isChecked():
- self.i_slope()
-
+ self.i_slope()
+
# Downloading and processing on theia platform
# A check box to get number download available images
if self.ui.checkBox_listing.isChecked():
-
+
if self.ui.checkBox_download.isChecked():
#Â To launch the downloading
dd = 1
-
+
self.i_download(dd) #Â Launch image listing and downloading if dd = 1
self.set_variable() #Â to write in the line edit about number download available images
-
+
#Â Check box to launch the image processing
if self.ui.checkBox_processing.isChecked():
# Another check box to launch VHRS texture processing. If checked, vs = 1.
if self.ui.checkBox_VHRS.isChecked():
vs = 1
- self.i_images_processing(vs) #Â function to launch the image processing
-
+ self.i_images_processing(vs) #Â function to launch the image processing
+
# To launch the image processing without dowloading but with the images in a main folder
# Without internet connection
if not self.ui.checkBox_download.isChecked() and self.ui.checkBox_processing.isChecked():
-
+
# Launch pre-processing without downloading
self.i_glob()
# Another check box to launch VHRS texture processing. If checked, vs = 1.
if self.ui.checkBox_VHRS.isChecked():
vs = 1
- self.i_images_processing(vs) #Â function to launch the image processing
-
+ self.i_images_processing(vs) #Â function to launch the image processing
+
# To launch texture processing only
if not self.ui.checkBox_listing.isChecked() and not self.ui.checkBox_processing.isChecked() and self.ui.checkBox_VHRS.isChecked():
-
+
self.i_vhrs()
-
- #Â Compute optimal threshold
+
+ #Â Compute optimal threshold
if self.ui.checkBox_threshold.isChecked():
-
+
if self.ui.radioButton_rf.isChecked():
self.i_sample_rf()
elif self.ui.radioButton_s.isChecked():
self.i_sample()
-
- #Â Classification processing
+
+ #Â Classification processing
if self.ui.radioButton_rf.isChecked():
-
+
if self.ui.checkBox_classifier_3.isChecked():
-
+
self.out_fieldname_carto = self.out_fieldname_carto
- self.out_fieldtype_carto = self.out_fieldtype_carto
+ self.out_fieldtype_carto = self.out_fieldtype_carto
self.i_classifier_rf()
self.i_validate()
-
+
elif self.ui.radioButton_s.isChecked():
-
- if self.ui.checkBox_classifier_1.isChecked() :
-
+
+ if self.ui.checkBox_classifier_1.isChecked() :
+
self.out_fieldname_carto = self.out_fieldname_carto[:3]
self.out_fieldtype_carto = self.out_fieldtype_carto[:3]
self.i_classifier_s()
self.i_validate()
-
+
if self.ui.checkBox_classifier_2.isChecked() :
-
+
self.out_fieldname_carto = self.out_fieldname_carto[:4]
- self.out_fieldtype_carto = self.out_fieldtype_carto[:4]
+ self.out_fieldtype_carto = self.out_fieldtype_carto[:4]
self.i_classifier_s()
self.i_validate()
-
+
if self.ui.checkBox_classifier_3.isChecked():
-
+
self.out_fieldname_carto = self.out_fieldname_carto
- self.out_fieldtype_carto = self.out_fieldtype_carto
+ self.out_fieldtype_carto = self.out_fieldtype_carto
self.i_classifier_s()
self.i_validate()
-
+
if self.current_mode == Constantes.SIMPLE_MODE:
-
- # Compute a output slope raster
+
+ # Compute a output slope raster
if self.path_mnt :
self.i_slope()
# Save the sample features
self.add_sample()
-
+
# Look at if the the images has been already downloaded, download them otherwise
self.i_download(self.ui.ignore_download.isChecked())
-
- #Â function to launch the image processing
+
+ #Â function to launch the image processing
self.i_images_processing()
- #Â Compute optimal threshold
+ os.system("clear")
+
+ self.logger.debug("Début sample")
+
+ #Â Compute optimal threshold
self.i_sample_rf()
- #Â Classification processing
+ self.logger.debug("Fin sample")
+
+ os.system("clear")
+
+ self.logger.debug("Début classifier")
+
+ #Â Classification processing
self.i_classifier_rf()
+ self.logger.debug("Fin classifier")
+
+ os.system("clear")
+
+ self.logger.debug("Début validation")
+
self.i_validate()
+ self.logger.debug("Fin validation")
+
# Clear variables after processing
#self.clear_sample()
self.out_fieldname_carto = ['ID', 'AREA']
@@ -954,37 +968,37 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
# Images after processing images
self.out_ndvistats_folder_tab = defaultdict(list)
-
+
Processing.__init__(self)#Â Initialize variable without to close and launch again the application
-
+
# End of the processus
endTime = time.time()
self.logger.info('Outputted to File in {0} secondes'.format(endTime - startTime))
nb_day_processing = int(time.strftime('%d', time.gmtime(endTime - startTime))) - 1
self.logger.info("That is {0} day(s) {1}".format(nb_day_processing, time.strftime('%Hh %Mmin%S', time.gmtime(endTime - startTime))))
-
+
def open_backup(self, test=None):
"""
Function to load input text in every fields. The input file must be a XML file.
"""
# in_backup = QtWidgets.QFileDialog.getOpenFileName(self, "Open backup", os.getcwd(), '*.xml')[0]
-
+
if test is False :
in_backup = QtWidgets.QFileDialog.getOpenFileName(self, "Open backup", os.getcwd(), '*.xml')[0]
else :
in_backup = test
-
+
if in_backup and len(in_backup) > 0 :
# Parse the xml file if the user choose a file
tree = ET.parse(str(in_backup))
-
+
if tree.find("Multi_process").text == '1':
self.ui.checkBox_multiprocess.setChecked(True)
else:
self.ui.checkBox_multiprocess.setChecked(False)
-
+
pr = tree.find("Tab[@id='Processing_raster']")
try:
@@ -1002,7 +1016,7 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.logger.debug('Not year images')
self.ui.lineEdit_area_path.setText(pr.find("Area_path").text)
-
+
if self.current_mode == Constantes.EXPERT_MODE:
if pr.find("Images_available").text == '1':
self.ui.checkBox_listing.setChecked(True)
@@ -1012,13 +1026,13 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.ui.checkBox_download.setChecked(True)
else:
self.ui.checkBox_download.setChecked(False)
-
+
try:
self.ui.lineEdit_user.setText(pr.find("Username").text)
self.ui.lineEdit_password.setText(pr.find("Password").text)
except:
self.logger.debug('Not username or password Theia')
-
+
self.f_proxy()
try:
pp = pr.find("Proxy[@id='Proxy']")
@@ -1035,7 +1049,7 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
except AttributeError:
self.logger.debug('Not proxy')
self.w_proxy.close_window()
-
+
if self.current_mode == Constantes.EXPERT_MODE:
if pr.find("Img_processing").text == '1':
self.ui.checkBox_processing.setChecked(True)
@@ -1044,25 +1058,25 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
if pr.find("VHRS_checked").text == '1':
self.ui.checkBox_VHRS.setChecked(True)
else:
- self.ui.checkBox_VHRS.setChecked(False)
-
+ self.ui.checkBox_VHRS.setChecked(False)
+
try:
self.ui.lineEdit_VHRS.setText(pr.find("VHRS").text)
except:
self.logger.debug('Not VHRS image')
-
+
if self.current_mode == Constantes.EXPERT_MODE:
if pr.find("MNT_checked").text == '1':
self.ui.checkBox_MNT.setChecked(True)
else:
- self.ui.checkBox_MNT.setChecked(False)
-
+ self.ui.checkBox_MNT.setChecked(False)
+
try:
self.ui.lineEdit_MNT.setText(pr.find("MNT").text)
except:
self.logger.debug('Not MNT')
-
- ps = tree.find("Tab[@id='Processing_sample']")
+
+ ps = tree.find("Tab[@id='Processing_sample']")
if self.current_mode == Constantes.EXPERT_MODE:
try:
for sple_n in ps.iter("Sample"):
@@ -1085,7 +1099,7 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.add_sample()
except:
self.logger.debug('Not sample')
-
+
elif self.current_mode == Constantes.SIMPLE_MODE:
# RPG
sple_n = ps[0]
@@ -1095,7 +1109,7 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.ui.lineEdit_select_sample_class_1.setText(sple_n.find("Classname_1").text)
self.ui.lineEdit_select_sample_class_2.setText(sple_n.find("Classname_2").text)
self.ui.lineEdit_select_sample_nb_poly.setText(sple_n.find("Nb_polygones").text)
-
+
# To Grass/wooden
sple_n = ps[1]
self.ui.lineEdit_sample_path_2.setText(sple_n.find("Sample_path").text)
@@ -1103,8 +1117,8 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.ui.lineEdit_select_sample_fieldname_4.setText(sple_n.find("Fieldname_2").text)
self.ui.lineEdit_select_sample_class_3.setText(sple_n.find("Classname_1").text)
self.ui.lineEdit_select_sample_class_4.setText(sple_n.find("Classname_2").text)
- self.ui.lineEdit_select_sample_nb_poly_2.setText(sple_n.find("Nb_polygones").text)
-
+ self.ui.lineEdit_select_sample_nb_poly_2.setText(sple_n.find("Nb_polygones").text)
+
# To wooden
sple_n = ps[2]
self.ui.lineEdit_sample_path_3.setText(sple_n.find("Sample_path").text)
@@ -1113,13 +1127,13 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.ui.lineEdit_select_sample_class_5.setText(sple_n.find("Classname_1").text)
self.ui.lineEdit_select_sample_class_6.setText(sple_n.find("Classname_2").text)
self.ui.lineEdit_select_sample_nb_poly_3.setText(sple_n.find("Nb_polygones").text)
-
+
if self.current_mode == Constantes.EXPERT_MODE:
if ps.find("Threshold_checked").text == '1':
self.ui.checkBox_threshold.setChecked(True)
else:
- self.ui.checkBox_threshold.setChecked(False)
-
+ self.ui.checkBox_threshold.setChecked(False)
+
c = tree.find("Tab[@id='Classification']")
try:
@@ -1136,15 +1150,15 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
if len(c) == 5:
self.ui.checkBox_classifier_1.setChecked(True)
self.ui.lineEdit_fieldname_1.setText(c.find("Output_fieldname_1").text)
- index_fieldname_1 = self.ui.comboBox_fieldname_1.findText(c.find("Output_type_1").text)
+ index_fieldname_1 = self.ui.comboBox_fieldname_1.findText(c.find("Output_type_1").text)
self.ui.comboBox_fieldname_1.setCurrentIndex(index_fieldname_1)
elif len(c) == 7:
self.ui.checkBox_classifier_2.setChecked(True)
self.ui.lineEdit_fieldname_12.setText(c.find("Output_fieldname_1").text)
self.ui.lineEdit_fieldname_2.setText(c.find("Output_fieldname_2").text)
- index_fieldname_12 = self.ui.comboBox_fieldname_12.findText(c.find("Output_type_1").text)
+ index_fieldname_12 = self.ui.comboBox_fieldname_12.findText(c.find("Output_type_1").text)
self.ui.comboBox_fieldname_12.setCurrentIndex(index_fieldname_12)
- index_fieldname_2 = self.ui.comboBox_fieldname_2.findText(c.find("Output_type_2").text)
+ index_fieldname_2 = self.ui.comboBox_fieldname_2.findText(c.find("Output_type_2").text)
self.ui.comboBox_fieldname_2.setCurrentIndex(index_fieldname_2)
elif len(c) == 11:
self.ui.checkBox_classifier_3.setChecked(True)
@@ -1152,43 +1166,43 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
self.ui.lineEdit_fieldname_23.setText(c.find("Output_fieldname_2").text)
self.ui.lineEdit_fieldname_3.setText(c.find("Output_fieldname_3").text)
self.ui.lineEdit_fieldname_4.setText(c.find("Output_fieldname_4").text)
- index_fieldname_13 = self.ui.comboBox_fieldname_13.findText(c.find("Output_type_1").text)
+ index_fieldname_13 = self.ui.comboBox_fieldname_13.findText(c.find("Output_type_1").text)
self.ui.comboBox_fieldname_13.setCurrentIndex(index_fieldname_13)
- index_fieldname_23 = self.ui.comboBox_fieldname_23.findText(c.find("Output_type_2").text)
+ index_fieldname_23 = self.ui.comboBox_fieldname_23.findText(c.find("Output_type_2").text)
self.ui.comboBox_fieldname_23.setCurrentIndex(index_fieldname_23)
- index_fieldname_3 = self.ui.comboBox_fieldname_3.findText(c.find("Output_type_3").text)
+ index_fieldname_3 = self.ui.comboBox_fieldname_3.findText(c.find("Output_type_3").text)
self.ui.comboBox_fieldname_3.setCurrentIndex(index_fieldname_3)
- index_fieldname_4 = self.ui.comboBox_fieldname_4.findText(c.find("Output_type_4").text)
+ index_fieldname_4 = self.ui.comboBox_fieldname_4.findText(c.find("Output_type_4").text)
self.ui.comboBox_fieldname_4.setCurrentIndex(index_fieldname_4)
-
+
# Classification mode
if c.find("Classification_method").text == '1':
self.ui.radioButton_rf.setChecked(True)
else:
self.ui.radioButton_s.setChecked(True)
-
+
def save_backup(self):
"""
Function to save input text in every fields.
The output file must be a XML file.
"""
-
+
out_backup = QtWidgets.QFileDialog.getSaveFileName(self, "Save backup", os.getcwd(), '*.xml')[0]
#Â if the user has forgotten to put .shp at the end of the output xml
if not out_backup.endswith('.xml'):
out_backup = out_backup + '.xml'
-
+
root = ET.Element("Data_filled")
-
+
if self.ui.checkBox_multiprocess.isChecked():
ET.SubElement(root, "Multi_process", type = "int").text = str(1)
else:
ET.SubElement(root, "Multi_process", type = "int").text = str(0)
-
+
doc = ET.SubElement(root, "Tab", id="Processing_raster")
ET.SubElement(doc, "Principal_folder", type = "str").text = "%s" % self.ui.lineEdit_principal_folder.text()
-
+
if self.current_mode == Constantes.EXPERT_MODE:
ET.SubElement(doc, "Captor", type = "str").text = "%s" % self.ui.comboBox_captor.currentText()
else:
@@ -1196,7 +1210,7 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
ET.SubElement(doc, "Year_images", type = "str").text = "%s" % self.ui.lineEdit_year_images.text()
ET.SubElement(doc, "Area_path", type = "str").text = "%s" % self.ui.lineEdit_area_path.text()
-
+
if self.current_mode == Constantes.EXPERT_MODE:
if self.ui.checkBox_listing.isChecked():
ET.SubElement(doc, "Images_available", type = "int").text = str(1)
@@ -1209,7 +1223,7 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
else:
ET.SubElement(doc, "Images_available", type = "int").text = str(0)
ET.SubElement(doc, "Download", type = "int").text = str(0)
-
+
ET.SubElement(doc, "Username", type = "str").text = "%s" % self.ui.lineEdit_user.text()
ET.SubElement(doc, "Password", type = "str").text = "%s" % self.ui.lineEdit_password.text()
if self.w_proxy is None:
@@ -1227,13 +1241,13 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
ET.SubElement(sub_proxy, "Proxy_adress", type = "str").text = "%s" % self.w_proxy.proxy
ET.SubElement(sub_proxy, "Proxy_login", type = "str").text = "%s" % self.w_proxy.login_proxy
ET.SubElement(sub_proxy, "Proxy_password", type = "str").text = "%s" % self.w_proxy.password_proxy
-
+
if self.current_mode == Constantes.EXPERT_MODE:
if self.ui.checkBox_processing.isChecked():
ET.SubElement(doc, "Img_processing", type = "int").text = str(1)
else:
ET.SubElement(doc, "Img_processing", type = "int").text = str(0)
-
+
if self.ui.checkBox_VHRS.isChecked():
ET.SubElement(doc, "VHRS_checked", type = "int").text = str(1)
else:
@@ -1241,9 +1255,9 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
else:
ET.SubElement(doc, "Img_processing", type = "int").text = str(1)
ET.SubElement(doc, "VHRS_checked", type = "int").text = str(1)
-
+
ET.SubElement(doc, "VHRS", type = "str").text = "%s" % self.ui.lineEdit_VHRS.text()
-
+
if self.current_mode == Constantes.EXPERT_MODE:
if self.ui.checkBox_MNT.isChecked():
ET.SubElement(doc, "MNT_checked", type = "int").text = str(1)
@@ -1254,9 +1268,9 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
ET.SubElement(doc, "MNT_checked", type = "int").text = str(1)
else:
ET.SubElement(doc, "MNT_checked", type = "int").text = str(0)
-
+
ET.SubElement(doc, "MNT", type = "str").text = "%s" % self.ui.lineEdit_MNT.text()
-
+
doc = ET.SubElement(root, "Tab", id="Processing_sample")
if self.current_mode == Constantes.EXPERT_MODE:
for sa in range(len(self.sample_name)):
@@ -1269,11 +1283,11 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
ET.SubElement(sub_doc, "Nb_polygones", type = "str").text = self.list_nb_sample[sa]
ET.SubElement(sub_doc, "RPG", type = "int").text = str(self.rpg_tchek[sa])
try:
- #Â To enter a sample raster if the first tab doesn't launch before
+ #Â To enter a sample raster if the first tab doesn't launch before
if self.img_sample[sa] == 1:
ET.SubElement(sub_doc, "Img_sample", type = "str").text = self.raster_path[sa]
except:
- self.logger.debug('Not sample raster only !')
+ self.logger.debug('Not sample raster only !')
else:
# RPG
sub_doc = ET.SubElement(doc, "Sample", id="Sample_0")
@@ -1284,7 +1298,7 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
ET.SubElement(sub_doc, "Classname_2", type = "str").text = "%s" % self.ui.lineEdit_select_sample_class_2.text()
ET.SubElement(sub_doc, "Nb_polygones", type = "str").text = "%s" % self.ui.lineEdit_select_sample_nb_poly.text()
ET.SubElement(sub_doc, "RPG", type = "int").text = str(1)
-
+
# To Grass/wooden
sub_doc = ET.SubElement(doc, "Sample", id="Sample_1")
ET.SubElement(sub_doc, "Sample_path", type = "str").text = "%s" % self.ui.lineEdit_sample_path_2.text()
@@ -1294,8 +1308,8 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
ET.SubElement(sub_doc, "Classname_2", type = "str").text = "%s" % self.ui.lineEdit_select_sample_class_4.text()
ET.SubElement(sub_doc, "Nb_polygones", type = "str").text = "%s" % self.ui.lineEdit_select_sample_nb_poly_2.text()
ET.SubElement(sub_doc, "RPG", type = "int").text = str(0)
-
- # To wooden
+
+ # To wooden
sub_doc = ET.SubElement(doc, "Sample", id="Sample_2")
ET.SubElement(sub_doc, "Sample_path", type = "str").text = "%s" % self.ui.lineEdit_sample_path_3.text()
ET.SubElement(sub_doc, "Fieldname_1", type = "str").text = "%s" % self.ui.lineEdit_select_sample_fieldname_5.text()
@@ -1303,8 +1317,8 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
ET.SubElement(sub_doc, "Classname_1", type = "str").text = "%s" % self.ui.lineEdit_select_sample_class_5.text()
ET.SubElement(sub_doc, "Classname_2", type = "str").text = "%s" % self.ui.lineEdit_select_sample_class_6.text()
ET.SubElement(sub_doc, "Nb_polygones", type = "str").text = "%s" % self.ui.lineEdit_select_sample_nb_poly_3.text()
- ET.SubElement(sub_doc, "RPG", type = "int").text = str(0)
-
+ ET.SubElement(sub_doc, "RPG", type = "int").text = str(0)
+
if self.current_mode == Constantes.EXPERT_MODE:
if self.ui.checkBox_threshold.isChecked():
ET.SubElement(doc, "Threshold_checked", type = "int").text = str(1)
@@ -1312,33 +1326,33 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
ET.SubElement(doc, "Threshold_checked", type = "int").text = str(0)
else:
ET.SubElement(doc, "Threshold_checked", type = "int").text = str(1)
-
+
doc = ET.SubElement(root, "Tab", id="Classification")
ET.SubElement(doc, "Segmentation_path", type = "str").text = "%s" % self.ui.lineEdit_segmentation.text()
ET.SubElement(doc, "Output_path", type = "str").text = "%s" % self.ui.lineEdit_output.text()
-
+
if self.current_mode == Constantes.EXPERT_MODE:
-
+
if self.ui.checkBox_classifier_1.isChecked():
ET.SubElement(doc, "Output_fieldname_1", type = "str").text = "%s" % self.ui.lineEdit_fieldname_1.text()
ET.SubElement(doc, "Output_type_1", type = "str").text = "%s" % self.ui.comboBox_fieldname_1.currentText()
-
+
if self.ui.checkBox_classifier_2.isChecked():
ET.SubElement(doc, "Output_fieldname_1", type = "str").text = "%s" % self.ui.lineEdit_fieldname_12.text()
- ET.SubElement(doc, "Output_type_1", type = "str").text = "%s" % self.ui.comboBox_fieldname_12.currentText()
+ ET.SubElement(doc, "Output_type_1", type = "str").text = "%s" % self.ui.comboBox_fieldname_12.currentText()
ET.SubElement(doc, "Output_fieldname_2", type = "str").text = "%s" % self.ui.lineEdit_fieldname_2.text()
ET.SubElement(doc, "Output_type_2", type = "str").text = "%s" % self.ui.comboBox_fieldname_2.currentText()
-
+
if self.ui.checkBox_classifier_3.isChecked():
ET.SubElement(doc, "Output_fieldname_1", type = "str").text = "%s" % self.ui.lineEdit_fieldname_13.text()
- ET.SubElement(doc, "Output_type_1", type = "str").text = "%s" % self.ui.comboBox_fieldname_13.currentText()
+ ET.SubElement(doc, "Output_type_1", type = "str").text = "%s" % self.ui.comboBox_fieldname_13.currentText()
ET.SubElement(doc, "Output_fieldname_2", type = "str").text = "%s" % self.ui.lineEdit_fieldname_23.text()
ET.SubElement(doc, "Output_type_2", type = "str").text = "%s" % self.ui.comboBox_fieldname_23.currentText()
ET.SubElement(doc, "Output_fieldname_3", type = "str").text = "%s" % self.ui.lineEdit_fieldname_3.text()
ET.SubElement(doc, "Output_type_3", type = "str").text = "%s" % self.ui.comboBox_fieldname_3.currentText()
ET.SubElement(doc, "Output_fieldname_4", type = "str").text = "%s" % self.ui.lineEdit_fieldname_4.text()
ET.SubElement(doc, "Output_type_4", type = "str").text = "%s" % self.ui.comboBox_fieldname_4.currentText()
-
+
# Classification mode
if self.ui.radioButton_rf.isChecked():
ET.SubElement(doc, "Classification_method", type = "int").text = str(1)
@@ -1346,7 +1360,7 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
ET.SubElement(doc, "Classification_method", type = "int").text = str(0)
else:
ET.SubElement(doc, "Output_fieldname_1", type = "str").text = "NIVEAU_1"
- ET.SubElement(doc, "Output_type_1", type = "str").text = "String"
+ ET.SubElement(doc, "Output_type_1", type = "str").text = "String"
ET.SubElement(doc, "Output_fieldname_2", type = "str").text = "NIVEAU_2"
ET.SubElement(doc, "Output_type_2", type = "str").text = "String"
ET.SubElement(doc, "Output_fieldname_3", type = "str").text = "NIVEAU_3"
@@ -1354,17 +1368,17 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
ET.SubElement(doc, "Output_fieldname_4", type = "str").text = "POURC"
ET.SubElement(doc, "Output_type_4", type = "str").text = "Real"
ET.SubElement(doc, "Classification_method", type = "int").text = str(1)
-
+
tree = ET.ElementTree(root)
#Â Write in a xml file
tree.write(str(out_backup), encoding="UTF-8",xml_declaration=True, pretty_print=True)
-
+
def help_tools(self):
"""
Function to open html help
"""
webbrowser.open('file://' + os.getcwd() + '/Documentation/methode_tuto.html#tutoriels-interface')
-
+
def change_mode(self, new_mode):
"""
@@ -1393,23 +1407,23 @@ class PHYMOBAT(QtWidgets.QMainWindow, Processing):
Function to open a new window 'Alert' because user forgotten to declare study area.
"""
self.w_study_area.show()
-
+
def forget_raster_sample(self):
"""
Function to open a new window 'Alert' because user forgotten to declare rasters or samples.
- """
+ """
self.w_forget.show()
-
+
def close_button(self):
"""
Function to close the interface.
"""
self.close()
-
+
if __name__ == "__main__":
-
+
app = QtWidgets.QApplication(sys.argv)
myapp = PHYMOBAT()
myapp.show()
-
+
sys.exit(app.exec_())
diff --git a/Processing.py b/Processing.py
index 9d833cb..218d330 100644
--- a/Processing.py
+++ b/Processing.py
@@ -3,17 +3,17 @@
#
# This file is part of PHYMOBAT 2.0.
# Copyright 2016 Sylvio Laventure (IRSTEA - UMR TETIS)
-#
+#
# PHYMOBAT 2.0 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
-#
+#
# PHYMOBAT 2.0 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
-#
+#
# You should have received a copy of the GNU General Public License
# along with PHYMOBAT 2.0. If not, see <http://www.gnu.org/licenses/>.
@@ -22,6 +22,7 @@ import numpy as np
import subprocess
from sklearn.ensemble import RandomForestClassifier
from sklearn import tree
+import pydot
try :
import ogr, gdal
@@ -52,19 +53,18 @@ from multiprocessing import Process
from multiprocessing.managers import BaseManager, DictProxy
class Processing(object):
-
"""
Main processing. This class launch the others system classes. It take into account
- CarHab classification method MOBA.
-
+ CarHab classification method MOBA.
+
This way is broken down into 3 parts :
- Image Processing (Search, download and processing)
- Vector Processing (Optimal threshold, Sample processing)
- - Classification
- - Validation
-
+ - Classification
+ - Validation
+
**Main parameters**
-
+
:param captor_project: Satellite captor name
:type captor_project: str
:param classif_year: Classification year
@@ -83,25 +83,25 @@ class Processing(object):
:type path_mnt: str
:param path_segm: Segmentation shapefile
:type path_segm: str
-
+
**Id information to download on theia platform**
-
+
:param user: Connexion Username
:type user: str
:param password: Connexion Password
:type password: str
-
+
**Output parameters**
-
+
:param output_name_moba: Output classification shapefile
:type output_name_moba: str
:param out_fieldname_carto: Output shapefile field name
:type out_fieldname_carto: list of str
:param out_fieldtype_carto: Output shapefile field type
:type out_fieldtype_carto: list of str (eval ogr pointer)
-
+
**Sample parameters**
-
+
:param fieldname_args: Sample field names 2 by 2
:type fieldname_args: list of str
:param class_args: Sample class names 2 by 2
@@ -110,18 +110,18 @@ class Processing(object):
:type sample_name: list of str
:param list_nb_sample: Number of polygons for every sample
:type list_nb_sample: list of int
-
+
**Multi-processing parameters**
-
+
:param mp: Boolean variable -> 0 or 1.
-
+
- 0 means, not multi-processing
- 1 means, launch process with multi-processing
:type mp: int
"""
-
+
def __init__(self):
-
+
# Used variables
self.captor_project = ''
self.classif_year = ''
@@ -132,16 +132,16 @@ class Processing(object):
self.path_mnt = ''
self.path_segm = ''
self.output_name_moba = ''
-
+
self.w_proxy = None # For the "Proxy window"
-
+
# Id information to download on theia platform
self.user = ''
self.password = ''
# List of output raster path
self.raster_path = defaultdict(dict)
-
+
# TODO : Change index of the classes -> Harbacées 6 / Ligneux 7 by Agriculuture 4 / Eboulis 5
# Class name
self.in_class_name = ['Non Vegetation semi-naturelle', 'Vegetation semi-naturelle',\
@@ -149,7 +149,7 @@ class Processing(object):
'Ligneux mixtes', 'Ligneux denses',\
'Agriculture', 'Eboulis', \
'Forte phytomasse', 'Moyenne phytomasse', 'Faible phytomasse']
-
+
# Sample field names 2 by 2
self.fieldname_args = []
# 'CODE_GROUP', 'CODE_GROUP',\
@@ -161,7 +161,7 @@ class Processing(object):
# '1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 20, 21, 22, 23, 24, 26, 28', '18',\
# 'H','LF, LO',\
# 'LF', 'LO']
-
+
# Decision tree combination
self.tree_direction = [[0],\
[0],\
@@ -173,105 +173,104 @@ class Processing(object):
# ..., ['Semi-naturelles', 'Ligneux', 'Ligneux denses']]
# Slope degrees
self.slope_degree = 30
-
+
# Output shapefile field name
self.out_fieldname_carto = ['ID', 'AREA'] #, 'NIVEAU_1', 'NIVEAU_2', 'NIVEAU_3', 'POURC']
# Output shapefile field type
self.out_fieldtype_carto = [ogr.OFTString, ogr.OFTReal] #, ogr.OFTString, ogr.OFTString, ogr.OFTString, ogr.OFTReal]
-
+
# List of sample name path
self.sample_name = []
# List of number sample
self.list_nb_sample = []
# Number download available images
self.nb_avalaible_images = 0
-
+
# Multi-processing variable
self.mp = Constantes.MULTIPROCESSING_DISABLE
-
+
# Function followed
self.check_download = None
self.decis = {}
# Images after processing images
self.out_ndvistats_folder_tab = defaultdict(list)
-
+
# Validation shapefiles information
self.valid_shp = []
-
+
# Radom Forest Model
- # Set the parameters of this random forest from the estimator
+ # Set the parameters of this random forest from the estimator
self.rf = RandomForestClassifier(n_estimators=500, criterion='gini', max_depth=None, min_samples_split=2, \
min_samples_leaf=1, max_features='auto', \
bootstrap=True, oob_score=True)
-
- def i_tree_direction(self):
+
+ def i_tree_direction(self):
"""
- Interface function to can extract one level or two levels of the final classification
+ Interface function to can extract one level or two levels of the final classification
"""
if len(self.out_fieldname_carto) == 3:
self.tree_direction = [[0], [1]]
-
+
if len(self.out_fieldname_carto) == 4:
self.tree_direction = [[0], [0], [1, 2], [1, 3]]
-
+
def i_download(self, ignore_download=False):
"""
- Interface function to download archives on the website Theia Land. This function extract
+ Interface function to download archives on the website Theia Land. This function extract
the number of downloadable image with :func:`Archive.Archive.listing`.
-
+
Then, this function download :func:`Archive.Archive.download` and unzip :func:`Archive.Archive.decompress` images
in the archive folder (**folder_archive**).
"""
-
+
folder_archive = "{0}/{1}_PoleTheia".format(self.folder_processing, self.captor_project)
if not os.path.exists(folder_archive) :
os.makedirs(folder_archive)
self.check_download = Archive(self.captor_project, self.classif_year, self.path_area, folder_archive, self.w_proxy)
-
+
if not ignore_download :
self.nb_avalaible_images = self.check_download.listing()
self.check_download.download_auto(self.user, self.password)
-
+
self.check_download.decompress()
- def i_img_sat(self):
+ def i_img_sat(self):
"""
Interface function to processing satellite images:
-
+
1. Clip archive images and modify Archive class to integrate clip image path.
With :func:`Toolbox.clip_raster` in ``Toolbox`` module.
-
- 2. Search cloud's percentage :func:`RasterSat_by_date.RasterSat_by_date.pourc_cloud`,
+
+ 2. Search cloud's percentage :func:`RasterSat_by_date.RasterSat_by_date.pourc_cloud`,
select image and compute ndvi index :func:`RasterSat_by_date.RasterSat_by_date.calcul_ndvi`.
If cloud's percentage is greater than 40%, then not select and compute ndvi index.
-
- 3. Compute temporal stats on ndvi index [min, max, std, min-max]. With :func:`Toolbox.calc_serie_stats`
+
+ 3. Compute temporal stats on ndvi index [min, max, std, min-max]. With :func:`Toolbox.calc_serie_stats`
in ``Toolbox`` module.
-
4. Create stats ndvi raster and stats cloud raster.
-
+
>>> import RasterSat_by_date
>>> stats_test = RasterSat_by_date(class_archive, big_folder, one_date)
>>> stats_test.complete_raster(stats_test.create_raster(in_raster, stats_data, in_ds), stats_data)
"""
-
+
current_list = Toolbox()
current_list.vect = self.path_area
# Map projection of the image and the cloud mask
for clip_index, clip in enumerate(self.check_download.list_img):
-
+
current_list.image = clip[3]
-
- current_list.check_proj() # Check if projection is RFG93
+
+ current_list.check_proj() # Check if projection is RFG93
self.check_download.list_img[clip_index][3] = current_list.clip_raster() # Multispectral images
-
+
current_list.image = clip[4]
- current_list.check_proj() # Check if projection is RFG93
+ current_list.check_proj() # Check if projection is RFG93
self.check_download.list_img[clip_index][4] = current_list.clip_raster() # Cloud images
@@ -283,8 +282,8 @@ class Processing(object):
for date in self.check_download.single_date:
check_L8.mosaic_by_date(date)
-
- # Search cloud's percentage, select image and compute ndvi index
+
+ # Search cloud's percentage, select image and compute ndvi index
if check_L8.pourc_cloud() < Constantes.CLOUD_THRESHOLD :
tmp = date
check_L8.calcul_ndvi()
@@ -294,7 +293,7 @@ class Processing(object):
# Compute temporal stats on ndvi index [min, max, std, min-max]
spectral_trans = np.transpose(np.array(spectral_out, dtype=object))
- del spectral_out
+ del spectral_out
# stats_name = ['Min', 'Date', 'Max', 'Std', 'MaxMin']
stats_name = ['Min', 'Max']
@@ -311,12 +310,12 @@ class Processing(object):
Interface function to processing slope raster. From a MNT, and with a command line gdal,
this function compute slope in degrees :func:`Slope.Slope`.
"""
-
+
current_path_mnt = Toolbox()
current_path_mnt.image = self.path_mnt
current_path_mnt.vect = self.path_area
path_mnt = current_path_mnt.clip_raster()
-
+
study_slope = Slope(path_mnt)
# Call this function to compute slope raster
@@ -324,27 +323,27 @@ class Processing(object):
self.path_mnt = study_slope.out_mnt
current_path_mnt.logger.close()
-
+
def i_vhrs(self):
"""
- Interface function to processing VHRS images.
- It create two OTB texture images :
+ Interface function to processing VHRS images.
+ It create two OTB texture images :
func: `Vhrs.Vhrs` : SFS Texture and Haralick Texture
"""
############################## Create texture image ##############################
-
- # Clip orthography image
+
+ # Clip orthography image
current_path_ortho = Toolbox()
current_path_ortho.image = self.path_ortho
current_path_ortho.vect = self.path_area
current_path_ortho.output = "{0}/MosaiqueOrtho/Clip_{1}".format(self.folder_processing, os.path.basename(self.path_ortho))
-
+
self.path_ortho = current_path_ortho.output
path_ortho = current_path_ortho.clip_raster()
-
+
texture_irc = Vhrs(path_ortho, self.mp)
self.out_ndvistats_folder_tab['sfs'] = texture_irc.out_sfs
self.out_ndvistats_folder_tab['haralick'] = texture_irc.out_haralick
@@ -352,10 +351,10 @@ class Processing(object):
current_path_ortho.logger.close()
texture_irc.logger.close()
-
- def i_images_processing(self):
+
+ def i_images_processing(self):
"""
- Interface function to launch processing VHRS images : func:`i_vhrs`
+ Interface function to launch processing VHRS images : func:`i_vhrs`
and satellite images :func:`i_img_sat` in multi-processing.
"""
@@ -365,18 +364,18 @@ class Processing(object):
mgr.register('defaultdict', defaultdict, DictProxy)
mgr.start()
- self.out_ndvistats_folder_tab = mgr.defaultdict(list)
-
+ self.out_ndvistats_folder_tab = mgr.defaultdict(list)
+
p_img_sat = Process(target=self.i_img_sat)
p_vhrs = Process(target=self.i_vhrs)
self.logger.debug("Multiprocessing : {0}".format(self.mp))
-
+
if self.mp == Constantes.MULTIPROCESSING_DISABLE:
p_img_sat.start()
p_img_sat.join()
p_vhrs.start()
- p_vhrs.join()
+ p_vhrs.join()
else :
p_img_sat.start()
p_vhrs.start()
@@ -387,7 +386,7 @@ class Processing(object):
self.raster_path["Min"]["PATH"] = self.out_ndvistats_folder_tab['Min']
self.raster_path["Min"]["BAND"] = 1
-
+
for i in range(1,7) :
self.raster_path["SFS_{0}".format(i)]["PATH"] = self.out_ndvistats_folder_tab['sfs']
self.raster_path["SFS_{0}".format(i)]["BAND"] = i
@@ -395,24 +394,24 @@ class Processing(object):
for i in range(1,9) :
self.raster_path["HARALICK_{0}".format(i)]["PATH"] = self.out_ndvistats_folder_tab['haralick']
self.raster_path["HARALICK_{0}".format(i)]["BAND"] = i
-
+
# To slope, to extract scree
if self.path_mnt :
self.raster_path["MNT"]["PATH"] = self.path_mnt
self.raster_path["MNT"]["BAND"] = 1
-
+
self.raster_path["MAX"]["PATH"] = self.out_ndvistats_folder_tab['Max']
self.raster_path["MAX"]["BAND"] = 1
-
+
self.logger.info("End of images processing !")
-
- def i_rpg(self, path_rpg):
+
+ def i_rpg(self, path_rpg):
"""
Interface function to extract mono rpg crops.
-
+
@param path_rpg: Input RPG shapefile.
@type path_rpg: str
-
+
@returns: str -- variable **Rpg.vector_used**, output no duplicated crops shapefile (path).
"""
@@ -420,10 +419,10 @@ class Processing(object):
format(self.path_folder_dpt, self.folder_processing, self.captor_project)
dossier_rpg = "{0}/RPG".format(self.folder_processing)
-
+
# Extract rpg crops
mono_sample = Rpg(path_rpg, self.path_area)
-
+
mono_sample.clip_vector(dossier_rpg)
mono_sample.vector_data()
@@ -440,25 +439,25 @@ class Processing(object):
mono_sample.logger.close()
return mono_sample.vector_used
-
+
def i_sample(self):
"""
- Interface function to compute threshold with various sample.
- It also extract a list of validation layer (shapefile)
- to compute the precision of the next classification : func:`i_validate`.
-
- It create samples 2 by 2 with kwargs field names and class :func:`Sample.Sample.create_sample`.
+ Interface function to compute threshold with various sample.
+ It also extract a list of validation layer (shapefile)
+ to compute the precision of the next classification : func:`i_validate`.
+
+ It create samples 2 by 2 with kwargs field names and class :func:`Sample.Sample.create_sample`.
Then, it compute zonal statistics by polygons :func:`Vector.Sample.zonal_stats`.
-
+
With zonal statistics computed, a optimal threshold is determined :
- func:`Seath.Seath.separability_and_threshold` that will print in a text file .lg
+ func:`Seath.Seath.separability_and_threshold` that will print in a text file .lg
in the main folder.
-
+
.. warning:: :func:`Seath.Seath.separability_and_threshold` does not always
allow to discriminate optimal threshold. Then, this function will be launch
at least ten time until it reaches a optimal threshold.
"""
-
+
# Compute threshold with various sample
i_s = 0
while i_s < 10:
@@ -483,24 +482,24 @@ class Processing(object):
sample_rd[sple].create_sample(**kwargs)
sample_rd[sple].zonal_stats((self.raster_path[round(sple/2)],\
self.list_band_outraster[round(sple/2)]))
-
+
# Add the validation shapefile
self.valid_shp.append([sample_rd[sple].vector_val, kwargs['fieldname'], kwargs['class']])
-
- # Search the optimal threshold by class
+
+ # Search the optimal threshold by class
# Open a text file to print stats of Seath method
- with open("{0}/log_J.lg".format(self.path_folder_dpt), "wb") as f :
+ with open("{0}/log_J.lg".format(self.path_folder_dpt), "wb") as f :
for th_seath in range(len(self.sample_name)):
self.decis[th_seath] = Seath()
self.decis[th_seath].value_1 = sample_rd[th_seath*2].stats_dict
self.decis[th_seath].value_2 = sample_rd[th_seath*2 + 1].stats_dict
self.decis[th_seath].separability_and_threshold()
-
+
# Print the J value in the text file .lg
f.write('For {0} :\n'.format(self.sample_name[th_seath]))
f.write('J = {0}\n'.format(self.decis[th_seath].J[0]))
f.write('The class 1 {0}\n'.format(self.decis[th_seath].threshold[0]))
-
+
i_s = 20
except Exception as e:
self.logger.error("Error 519 : {0}".format(e))
@@ -510,17 +509,16 @@ class Processing(object):
if i_s != 20 or True:
self.logger.error('Problem during the sample processing.')
sys.exit(1)
-
+
def i_sample_rf(self):
"""
This function build a random forest trees like model to create a final classification.
All of this using the method described in the : func:`i_validate` function and because
of sklearn module.
"""
-
+
X_rf = []
y_rf = []
- sample_rd = {}
self.liste_chemin = [self.out_ndvistats_folder_tab['Min'], self.out_ndvistats_folder_tab['sfs'],\
self.out_ndvistats_folder_tab['haralick'], self.out_ndvistats_folder_tab['Max'] ]
@@ -534,32 +532,32 @@ class Processing(object):
self.logger.debug("Creation Sample : {0} - {1} - {2}".format(\
self.sample_name[round(sple/2)], self.path_area, self.list_nb_sample[round(sple/2)]) )
- sample_rd[sple] = Sample(self.sample_name[round(sple/2)], self.path_area,\
+ sample_rd = Sample(self.sample_name[round(sple/2)], self.path_area,\
self.list_nb_sample[round(sple/2)])
- sample_rd[sple].clip_vector("{0}/{1}".format(self.folder_processing, os.path.basename(\
+ sample_rd.clip_vector("{0}/{1}".format(self.folder_processing, os.path.basename(\
os.path.dirname(self.sample_name[round(sple/2)]))))
-
- sample_rd[sple].vector_data()
- sample_rd[sple].output_folder = self.folder_processing
-
+
+ sample_rd.vector_data()
+ sample_rd.output_folder = self.folder_processing
+
self.logger.debug("kwargs : {0}".format(kwargs))
- sample_rd[sple].create_sample(**kwargs)
+ sample_rd.create_sample(**kwargs)
# Add the validation shapefile
- self.valid_shp.append([sample_rd[sple].vector_val, kwargs['fieldname'], kwargs['class']])
+ self.valid_shp.append([sample_rd.vector_val, kwargs['fieldname'], kwargs['class']])
items = list(self.raster_path.items())
self.logger.debug("Raster path items: {0}".format(self.raster_path.items()))
- sample_rd[sple].zonal_stats(self.liste_chemin)
+ sample_rd.zonal_stats(self.liste_chemin)
# To convert the dictionnary in a list
- for key, value in sample_rd[sple].stats_dict.items():
+ for key, value in sample_rd.stats_dict.items():
# X_rf.append([-10000 if (math.isnan(x) or math.isinf(x)) else x for x in value])
- # To set the grassland class of the RPG and PIAO (same class)
+ # To set the grassland class of the RPG and PIAO (same class)
if sple == 2 :
# y_rf.append(1)
pass
@@ -568,53 +566,61 @@ class Processing(object):
pass
else :
y_rf.append(sple)
- X_rf.append([-10000 if (x is None or math.isnan(x) or math.isinf(x)) else x for x in value])
-
- sample_rd[sple].logger.close()
+ # X_rf.append([-10000 if (x is None or math.isnan(x) or math.isinf(x)) else x for x in value])
+ X_rf.append([x for x in value if (x is not None and not math.isnan(x) and not math.isinf(x))])
+
+ sample_rd.logger.close()
+ sample_rd = None
- #Â Build a forest of trees from the samples
+ #Â Build a forest of trees from the samples
self.rf = self.rf.fit(X_rf, y_rf)
-
+
+ X_rf = None
+ y_rf = None
+
#Â Print in a file feature important
importance = self.rf.feature_importances_
importance = [(importance[x],x+1) for x in range(len(importance))]
importance.sort()
-
+
file_feat_import = "{0}/Feature_important_RF.ft".format(self.folder_processing)
if os.path.exists(file_feat_import):
os.remove(file_feat_import)
-
+
with open(file_feat_import, "w") as f_out :
f_out.write("{0}".format(importance))
-
+
#Â Print in a file decision tree
file_decisiontree = "{0}/Decision_tree.dot".format(self.folder_processing)
-
+ image_decisiontree = "{0}/Decision_tree.png".format(self.folder_processing)
+
if os.path.exists(file_decisiontree):
os.remove(file_decisiontree)
-
+
tree_in_forest = self.rf.estimators_[499]
with open(file_decisiontree, 'w') as my_file:
my_file = tree.export_graphviz(tree_in_forest, out_file = my_file)
- def i_classifier_rf(self):
+ (graph,) = pydot.graph_from_dot_file(file_decisiontree)
+ graph.write_png(image_decisiontree)
+
+ def i_classifier_rf(self):
"""
- Interface function to launch random forest classification with a input segmentation :
+ Interface function to launch random forest classification with a input segmentation :
func:`Segmentation.Segmentation`.
-
+
This function use the sklearn module to build the best of decision tree to extract classes.
The optimal threshold are stored by class **rf** variable in :func:`Processing.i_sample_rf`.
Then it computes zonal statistics by polygons for every images in multi-processing (if **mp** = 1).
"""
-
+
# Multiprocessing
mgr = BaseManager()
mgr.register('defaultdict', defaultdict, DictProxy)
mgr.start()
- multi_process_var = [] # Multi processing variable
-
+
# Extract final cartography
out_carto = Segmentation.Segmentation(self.path_segm, self.path_area)
@@ -633,7 +639,7 @@ class Processing(object):
# Stats backup file
file_stats = "{0}/Stats_raster_spectral_texture.stats".format(self.folder_processing)
-
+
p = []
kwargs = {}
X_out_rf = [] # Variable list to compute decision tree with random forest method
@@ -644,13 +650,15 @@ class Processing(object):
out_carto.stats_dict = mgr.defaultdict(list)
out_carto.zonal_stats(self.liste_chemin)
-
+
for key, value_seg in out_carto.stats_dict.items():
- true_value = [-10000 if (x is None or math.isnan(x) or math.isinf(x)) else x for x in value_seg]
+ # true_value = [-10000 if (x is None or math.isnan(x) or math.isinf(x)) else x for x in value_seg]
+ true_value = [x for x in value_seg if (x is not None and not math.isnan(x) and not math.isinf(x))]
+
X_out_rf.append(true_value)
-
+
f_out.write("{0}\n".format(true_value))
-
+
else:
# If the stats file exists already, open this file and append in the stats_dict variable
out_carto.stats_dict = defaultdict(list)
@@ -662,19 +670,20 @@ class Processing(object):
X_out_rf.append(eval(x_in.strip('\n')))
predicted_rf = self.rf.predict(X_out_rf)
+ X_out_rf = None
self.logger.debug("Taille sample_name : {0}".format(len(self.sample_name)))
-
+
# For the higher than level 1
if len(self.sample_name) > 2:
# Compute the biomass and density distribution
# Use 'out_carto.out_threshold' to know predicted in the segmentation class
out_carto.out_threshold["PREDICTION"] = predicted_rf
-
- # In the compute_biomass_density function, this variable used normally to define
+
+ # In the compute_biomass_density function, this variable used normally to define
#Â threshold of the classification with SEATH method is initialized
out_carto.compute_biomass_density('RF')
-
+
out_carto.class_tab_final = defaultdict(list)
for i_polyg in range(len(predicted_rf)):
i_final = 0
@@ -686,24 +695,27 @@ class Processing(object):
class_final = self.tree_direction[i_final]
i_final = len(self.tree_direction)
i_final = i_final + 1
-
+
if class_final == []:
class_final = [1, 2]
- # Set the class name because of predicted output formatted
+ # Set the class name because of predicted output formatted
out_carto.class_tab_final[i_polyg] = [self.in_class_name[f] for f in class_final] + \
[predicted_rf[i_polyg]] + [predicted_rf[i_polyg]]
-
+
#Â For the output line with one level, add a phantom level
#Â TODO : Replace constant by a variable in the condition 'while'
while len(out_carto.class_tab_final[i_polyg]) < 5:
out_carto.class_tab_final[i_polyg].insert(len(out_carto.class_tab_final[i_polyg])-2,'')
-
+
+ predicted_rf = None
# If there is more one fieldnames line edit fulled in classification tab
if len(self.sample_name) > 2:
# Compute biomass and density scale
out_carto.append_scale(self.in_class_name[2], 'self.stats_dict[ind_stats][3]/self.max_bio')
out_carto.append_scale(self.in_class_name[3], 'self.stats_dict[ind_stats][2]/self.max_wood_idm')
-
+
+ out_carto.stats_dict = None
+
#Â Rasterize RPG shapefile to complete the final shapefile
opt = {}
opt['Remove'] = 1
@@ -712,32 +724,33 @@ class Processing(object):
rpg_tif.clip_vector(os.path.dirname(self.sample_name[0]))
rpg_tif.vector_data()
- self.logger.debug(self.path_ortho)
+ self.logger.debug("path_ortho : {0}".format(self.path_ortho))
out_carto.stats_rpg_tif = out_carto.zonal_stats_pp(rpg_tif.layer_rasterization(self.path_ortho, 'CODE_GROUP'))
# Final cartography
out_carto.create_cartography(self.out_fieldname_carto, self.out_fieldtype_carto)
-
- def i_classifier_s(self):
+ out_carto = None
+
+ def i_classifier_s(self):
"""
- Interface function to launch decision tree classification with a input
+ Interface function to launch decision tree classification with a input
segmentation :func:`Segmentation.Segmentation`.
-
+
This function store optimal threshold by class **Segmentation.out_threshold**.
Then it computes zonal statistics by polygons for every images in multi-processing (if **mp** = 1).
- """
-
+ """
+
# Multiprocessing
mgr = BaseManager()
mgr.register('defaultdict', defaultdict, DictProxy)
mgr.start()
multi_process_var = [] # Multi processing variable
-
+
# Extract final cartography
- out_carto = Segmentation(self.path_segm, self.path_area)
+ out_carto = Segmentation(self.path_segm, self.path_area)
out_carto.output_file = self.output_name_moba
out_carto.out_class_name = self.in_class_name
-
+
for ind_th in range(len(self.sample_name)):
out_carto.out_threshold.append(self.decis[ind_th].threshold[0])
if '>' in self.decis[ind_th].threshold[0]:
@@ -747,7 +760,7 @@ class Processing(object):
# out_carto.zonal_stats((raster_path[ind_th], list_band_outraster[ind_th]))
multi_process_var.append([self.raster_path[ind_th], self.list_band_outraster[ind_th]])
-
+
# Compute zonal stats on slope raster
multi_process_var.append([self.raster_path[ind_th+1], self.list_band_outraster[ind_th+1]])
out_carto.out_threshold.append('<'+str(self.slope_degree)) # To agriculture
@@ -756,8 +769,8 @@ class Processing(object):
# Add class indexes
self.tree_direction[0].append(6)
self.tree_direction[0].append(7)
-
- # Compute zonal stats on Max NDVI raster
+
+ # Compute zonal stats on Max NDVI raster
try:
# out_carto.zonal_stats((raster_path[ind_th+1], list_band_outraster[ind_th+1]))
multi_process_var.append([self.raster_path[ind_th+2], self.list_band_outraster[ind_th+2]])
@@ -776,7 +789,7 @@ class Processing(object):
exist_stats = 0 # The sats file doesn't exist
# Open a stats backup to avoid computing again (Gain of time)
f_out = open(file_stats, "wb")
-
+
p = []
kwargs = {}
X_out_rf = [] # Variable list to compute decision tree with random forest method
@@ -787,23 +800,24 @@ class Processing(object):
kwargs['nb_img'] = len(multi_process_var)
p.append(Process(target=out_carto.zonal_stats, args=(multi_process_var[i], ), kwargs=kwargs))
p[i].start()
-
+
if self.mp == Constantes.MULTIPROCESSING_DISABLE:
p[i].join()
-
- if self.mp == Constantes.MULTIPROCESSING_ENABLE:
+
+ if self.mp == Constantes.MULTIPROCESSING_ENABLE:
for i in range(len(multi_process_var)):
p[i].join()
-
+
for key, value_seg in out_carto.stats_dict.items():
-
- true_value = [-10000 if (math.isnan(x) or math.isinf(x)) else x for x in value_seg]
+
+ # true_value = [-10000 if (math.isnan(x) or math.isinf(x)) else x for x in value_seg]
+ true_value = [x for x in value_seg if (not math.isnan(x) and not math.isinf(x))]
# Print rasters stats value in the text file .lg
f_out.write(str(true_value) + '\n')
-
+
# Close the output file
f_out.close()
-
+
else:
# If the stats file exists already, open this file and append in the stats_dict variable
out_carto.stats_dict = defaultdict(list)
@@ -813,36 +827,36 @@ class Processing(object):
index_in_stats = index_in_stats + 1
out_carto.stats_dict[index_in_stats] = eval(x_in.strip('\n'))
X_out_rf.append(eval(x_in.strip('\n')))
-
- # For the higher than level 1
+
+ # For the higher than level 1
if len(self.sample_name) > 2:
# Compute the biomass and density distribution
out_carto.compute_biomass_density()
-
+
out_carto.class_tab_final = defaultdict(list)
self.i_tree_direction()
out_carto.decision_tree(self.tree_direction)
-
+
# If there is more one fieldnames line edit fulled in classification tab
- if len(self.sample_name) > 2:
+ if len(self.sample_name) > 2:
# Compute biomass and density scale
out_carto.append_scale(self.in_class_name[2], 'self.stats_dict[ind_stats][3]/self.max_bio')
out_carto.append_scale(self.in_class_name[3], 'self.stats_dict[ind_stats][2]/self.max_wood_idm')
-
+
#Â Rasterize RPG shapefile to complete the final shapefile
opt = {}
opt['Remove'] = 1
rpg_tif = Vector(self.sample_name[0], self.path_area, **opt)
rpg_tif.layer_rasterization(self.path_ortho, 'CODE_GROUP')
-
+
# Final cartography
out_carto.mono_rpg_tif = "{0}.TIF".format(self.sample_name[0][:-4])
out_carto.create_cartography(self.out_fieldname_carto, self.out_fieldtype_carto)
-
+
def i_validate(self):
"""
- Interface to validate a classification. It going to rasterize the validation shapefile and the
- classification shapefile with :func:`layer_rasterization`.
+ Interface to validate a classification. It going to rasterize the validation shapefile and the
+ classification shapefile with :func:`layer_rasterization`.
Next, to compare pixel by pixel, the classification quality to built a confusion matrix in a csv file.
"""
@@ -855,10 +869,10 @@ class Processing(object):
complete_validate_shp = "{0}/validate.shp".format(os.path.dirname(self.valid_shp[0][0]))
#Â TODO: Set this method in the Precision_moba class
-
+
# Processing to rasterize the validate shapefile. 1) Merge sahpefiles 2) Rasterization
for val in self.valid_shp:
- if class_validate != 2:
+ if class_validate != 2:
# Grassland to 1
if (class_validate !=3 and len(self.out_fieldname_carto) != 4+2) or len(self.out_fieldname_carto) == 4+2:
# To the level 3 with woodeen to 4 and 5
@@ -866,15 +880,15 @@ class Processing(object):
# Self.valid_shp is a list of list. In this variable there is :
# [Shapefile path, fieldname classes, classnames]
opt = {}
- opt['Remove'] = 1 # To overwrite
-
+ opt['Remove'] = 1 # To overwrite
+
# Create a raster to valide the classification
# First time, create a new shapefile with a new field integer
sample_val = Sample(val[0], self.path_area, 1, **opt)
- opt['add_fieldname'] = 1
+ opt['add_fieldname'] = 1
opt['fieldname'] = 'CLASS_CODE'
opt['class'] = str(class_validate) # Add integer classes
-
+
# Set the new shapefile
val[0] = "{0}_.shp".format(val[0][:-4])
val[1] = opt['fieldname']
@@ -882,36 +896,36 @@ class Processing(object):
sample_val.clip_vector(sample_val.vector_folder)
sample_val.vector_data()
-
+
# Complete the new shapefile
sample_val.fill_sample(val[0], 0, **opt)
-
+
# Second time, merge the validate shapefile
if class_validate == 0 :
process_tocall_merge = ['ogr2ogr', '-overwrite', complete_validate_shp, val[0]]
elif class_validate > 0 :
process_tocall_merge = ['ogr2ogr', '-update', '-append', complete_validate_shp, \
val[0], '-nln', os.path.basename(str(complete_validate_shp[:-4]))]
-
+
subprocess.call(process_tocall_merge)
sample_val.logger.close()
-
- # Increrment variable
+
+ # Increment variable
class_validate = self.valid_shp.index(val) + 1
-
+
# Compute precision of the classification
- valid = Precision_moba(self.path_area, self.path_folder_dpt)
+ valid = Precision_moba(self.path_area, self.path_folder_dpt)
valid.complete_validation_shp = complete_validate_shp
valid.ex_raster = list(self.raster_path.items())[0][1]["PATH"]
# TODO: Call the RasterSat_by_Date class here instead of the Precision_moba class
self.logger.debug("Name moba : {0}".format(self.output_name_moba))
-
+
valid.preprocess_to_raster_precision(self.output_name_moba, 'FBPHY_CODE') # To the classification's data
valid.preprocess_to_raster_precision(complete_validate_shp, val[1]) # To the validation's data
-
+
# Compute precision on the output classification
valid.confus_matrix(valid.complete_img[0].raster_data(valid.img_pr[0])[0], valid.complete_img[1].raster_data(valid.img_pr[1])[0])
diff --git a/Sample.py b/Sample.py
index 266127d..0c2ce2b 100644
--- a/Sample.py
+++ b/Sample.py
@@ -3,17 +3,17 @@
#
# This file is part of PHYMOBAT 1.2.
# Copyright 2016 Sylvio Laventure (IRSTEA - UMR TETIS)
-#
+#
# PHYMOBAT 1.2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
-#
+#
# PHYMOBAT 1.2 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
-#
+#
# You should have received a copy of the GNU General Public License
# along with PHYMOBAT 1.2. If not, see <http://www.gnu.org/licenses/>.
@@ -31,9 +31,9 @@ except :
class Sample(Vector):
"""
- Vector class inherits the super vector class properties.
+ Vector class inherits the super vector class properties.
This class create training sample.
-
+
@param vector_used: Input/Output shapefile to clip (path)
@type vector_used: str
@@ -45,32 +45,32 @@ class Sample(Vector):
@param vector_val: Output shapefile to validate the futur classification
@type vector_val: str
-
+
@opt: Refer to the Vector class
"""
-
+
def __init__(self, used, cut, nb_sample, **opt):
"""
- Create a new 'Sample' instance
+ Create a new 'Sample' instance
"""
self.logger = Outils.Log('Log', 'Sample')
-
+
Vector.__init__(self, used, cut, **opt)
-
+
self._nb_sample = nb_sample
self.vector_val = ''
-
+
def create_sample(self, **kwargs):
"""
Function to create a sample shapefile of a specific class
-
+
:kwargs: **fieldname** (list of str) - Fieldname in the input shapefile (if the user want select polygons of the class names specific)
-
+
**class** (list of str) - class names in the input shapefile (with fieldname index).
Can use one or several classes like this --> example : [classname1, classname2, ...]
"""
-
+
kw_field = kwargs['fieldname'] if kwargs.get('fieldname') else ''
kw_classes = kwargs['class'] if kwargs.get('class') else ''
@@ -78,7 +78,7 @@ class Sample(Vector):
self.logger.debug("kw_classes : {0}".format(kw_classes))
self.output_folder = "{0}/{1}".format(self.output_folder, os.path.basename(os.path.dirname(self.vector_used)))
-
+
if not os.path.exists(self.output_folder) :
os.mkdir(self.output_folder)
@@ -89,7 +89,7 @@ class Sample(Vector):
else:
# The random sample without class name selected
random_sample = np.array(random.sample(range(self.data_source.GetLayer().GetFeatureCount()), self._nb_sample))
-
+
self.logger.debug("random_sample : {0}".format(random_sample))
# Output shapefile of the sample's polygons (path)
@@ -102,61 +102,51 @@ class Sample(Vector):
# Fill and create the sample shapefile
self.fill_sample(self.vector_used, random_sample[:round(len(random_sample)/2)])
-
+
# Output shapefile of the validate polygon (path)
- self.vector_val = "{0}val.shp".format(self.vector_used[:-6])
-
+ self.vector_val = "{0}val.shp".format(self.vector_used[:-6])
+
# Fill and create the validate polygons shapefile
self.fill_sample(self.vector_val, random_sample[round(len(random_sample)/2):])
- def select_random_sample(self, kw_field, kw_classes):
+ def select_random_sample(self, kw_field, kw_classes):
"""
Function to select id with class name specific only.
- This function is used in :func:`create_sample`
+ This function is used in :func:`create_sample`
@param kw_field: Field name in the input shapefile
@type kw_field: str
-
+
@param kw_classes: Class names in the input shapefile like this --> 'classname1, classname2'
@type kw_classes: str
-
+
@returns: list -- variable **select_id**, List of id with a class name specific.
"""
-
+
# Convert string in a list. For that, it remove
# space and clip this string with comma (Add everywhere if the script modified
# because the process work with a input string chain)
-
kw_classes = kw_classes.replace(' ','').split(',')
- self.logger.debug('kw_classes : {0}'.format(kw_classes))
-
+
#Â List of class name id
select_id = []
- shp_ogr = self.data_source.GetLayer()
+ layer = self.data_source.GetLayer()
- #Â Loop on input polygons
- in_feature = shp_ogr.SetNextByIndex(0) # Initialization
- in_feature = shp_ogr.GetNextFeature()
-
- while in_feature:
- #Â if polygon is a defined class name
- ## .replace('0','') to remove '0' in front of for example '1' (RPG -> '01')
- table_name_class = in_feature.GetField(self.field_names[self.field_names.index(kw_field)])
- # To avoid that the process crashed this part of the algorithm will be launch
- # if the field is contains characters
- if table_name_class != None :
- if in_feature.GetField(self.field_names[self.field_names.index(kw_field)]).replace('0','') in kw_classes:
-
- #Â Add id in the extract list
- select_id.append(in_feature.GetFID())
-
- in_feature.Destroy()
-
- in_feature = shp_ogr.GetNextFeature()
+ assert layer.GetFeatureCount() != 0, "Le shapefile : {0} est vide.".format(self.data_source.GetLayer().GetName())
+
+ for i in range(layer.GetFeatureCount()) :
+ feature = layer.GetFeature(i)
+
+ if feature.GetFieldIndex(self.field_names[self.field_names.index(kw_field)]) != -1 \
+ and not feature.GetField(self.field_names[self.field_names.index(kw_field)]) is None :
+ if feature.GetField(self.field_names[self.field_names.index(kw_field)]).replace('0','') in kw_classes :
+ select_id.append(i)
+
+ assert len(select_id) > 0, "Aucun polygone ne correspond."
return select_id
-
+
def fill_sample(self, output_sample, polygon, **opt):
"""
Function to fill and create the output sample shapefile.
@@ -165,15 +155,15 @@ class Sample(Vector):
@param output_sample: Path of the output shapefile
@type output_sample: str
-
+
@param polygon: Identity of the selected random polygons.
- If this variable = 0, the processing will take all polygons
- @type polygon: list or int
-
+ If this variable = 0, the processing will take all polygons
+ @type polygon: list or int
+
@opt: **add_fieldname** (int) - Variable to kown if add a field. By default non (0), if it have to add (1)
-
+
**fieldname** (str) - Fieldname to add in the input shapefile
-
+
**class** (int) - class names in integer to add in the input shapefile
"""
@@ -181,56 +171,56 @@ class Sample(Vector):
add_field = opt['add_fieldname'] if opt.get('add_fieldname') else 0
opt_field = opt['fieldname'] if opt.get('fieldname') else ''
opt_class = opt['class'] if opt.get('class') else 0
-
+
shp_ogr = self.data_source.GetLayer()
-
+
# To take all polygon
if type(polygon) == int:
polygon = range(shp_ogr.GetFeatureCount())
-
+
# Projection
# Import input shapefile projection
srsObj = shp_ogr.GetSpatialRef()
# Conversion to syntax ESRI
- srsObj.MorphToESRI()
-
+ srsObj.MorphToESRI()
+
## Remove the output shapefile if it exists
if os.path.exists(output_sample):
self.data_source.GetDriver().DeleteDataSource(output_sample)
-
+
out_ds = self.data_source.GetDriver().CreateDataSource(output_sample)
-
+
if out_ds is None:
self.logger.error('Could not create file')
sys.exit(1)
-
+
# Specific output layer
out_layer = out_ds.CreateLayer(output_sample, srsObj, geom_type=ogr.wkbMultiPolygon)
-
- # Add existing fields
+
+ # Add existing fields
for i in range(0, len(self.field_names)):
# use the input FieldDefn to add a field to the output
fieldDefn = shp_ogr.GetFeature(0).GetFieldDefnRef(self.field_names[i])
out_layer.CreateField(fieldDefn)
-
+
# In Option : Add a integer field
if add_field == 1:
new_field = ogr.FieldDefn(opt_field, 0)
out_layer.CreateField(new_field)
-
+
# Feature for the ouput shapefile
featureDefn = out_layer.GetLayerDefn()
-
+
# Loop on the input elements
- # Create a existing polygons in random list
+ # Create a existing polygons in random list
for cnt in polygon:
-
+
# Select input polygon by id
in_feature = shp_ogr.SetNextByIndex(cnt)
in_feature = shp_ogr.GetNextFeature()
-
+
# Extract input geometry
- geom = in_feature.GetGeometryRef()
+ geom = in_feature.GetGeometryRef()
# Create a new polygon
out_feature = ogr.Feature(featureDefn)
@@ -249,10 +239,10 @@ class Sample(Vector):
# Append polygon to the output shapefile
out_layer.CreateFeature(out_feature)
-
+
# Destroy polygons
- out_feature.Destroy()
+ out_feature.Destroy()
in_feature.Destroy()
-
+
# Close data
- out_ds.Destroy()
\ No newline at end of file
+ out_ds.Destroy()
diff --git a/Vector.py b/Vector.py
index e9fd31c..2cca534 100644
--- a/Vector.py
+++ b/Vector.py
@@ -3,39 +3,34 @@
#
# This file is part of PHYMOBAT 1.2.
# Copyright 2016 Sylvio Laventure (IRSTEA - UMR TETIS)
-#
+#
# PHYMOBAT 1.2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
-#
+#
# PHYMOBAT 1.2 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
-#
+#
# You should have received a copy of the GNU General Public License
# along with PHYMOBAT 1.2. If not, see <http://www.gnu.org/licenses/>.
import os, sys
import subprocess
import numpy as np
-import osgeo
-
-# try :
-# import ogr, gdal
-# except :
-# from osgeo import ogr, gdal
-
+from osgeo import ogr
import otbApplication as otb
from collections import *
+
import Outils
from RasterSat_by_date import RasterSat_by_date
class Vector():
- """
+ """
Vector class to extract a area, vector data and zonal statistic
-
+
@param vector_used: Input/Output shapefile to clip (path)
@type vector_used: str
@@ -59,10 +54,10 @@ class Vector():
@opt: **Remove** (int) - For the remove_shp variable
"""
-
+
def __init__(self, used, cut, **opt):
"""
- Create a new 'Vector' instance
+ Create a new 'Vector' instance
"""
if not hasattr(self, "logger") :
@@ -74,19 +69,19 @@ class Vector():
self.vector_cut = cut
self.vector_used = used
self.remove_shp = opt['Remove'] if opt.get('Remove') else 0
-
+
self.stats_dict = defaultdict(list)
-
+
def clip_vector(self, output_folder):
"""
Function to clip a vector with a vector
- """
+ """
if not os.path.exists(output_folder) :
os.makedirs(output_folder)
-
+
outclip = "{0}/Clip_{1}".format(output_folder, self.vector_name)
-
+
if not os.path.exists(outclip) or self.remove_shp == 1:
self.logger.info('Clip of {0}'.format(self.vector_name))
@@ -100,43 +95,43 @@ class Vector():
#Â Replace input filename by output filename
self.vector_used = outclip
-
+
def vector_data(self):
"""
- Function to extract vector layer information
+ Function to extract vector layer information
"""
try:
- self.data_source = osgeo.ogr.GetDriverByName('ESRI Shapefile').Open(self.vector_used, 0)
+ self.data_source = ogr.Open(self.vector_used)
self.logger.info('Shapefile opening : {0}'.format(self.data_source.GetLayer().GetName()))
except :
self.logger.error('Could not open file')
- sys.exit(1)
+ sys.exit(1)
# List of field name
self.field_names = [self.data_source.GetLayer().GetLayerDefn().GetFieldDefn(l).GetName() \
- for l in range(self.data_source.GetLayer().GetLayerDefn().GetFieldCount())]
+ for l in range(self.data_source.GetLayer().GetLayerDefn().GetFieldCount())]
def close_data(self):
"""
- Function to remove allocate memory
- """
-
+ Function to remove allocate memory
+ """
+
+ self.logger.info('Shapefile closing : {0}'.format(self.data_source.GetLayer().GetName()))
+
# Close data sources
self.data_source.Destroy()
-
- self.logger.info('Shapefile closing : {0}'.format(self.data_source.GetLayer().GetName()))
-
+
def zonal_stats(self, liste_chemin):
"""
Function to compute the mean in every polygons on a list images with otb
-
- :param liste_chemin : List input image path
- :type liste_chemin: list(string)
+
+ @param liste_chemin : List input image path
+ @type liste_chemin : list(string)
"""
-
+
self.logger.info("Compute stats 'mean' on {0}".format(os.path.split(self.vector_used)[1]))
-
+
zonal_stats = otb.Registry.CreateApplication("ZonalStatistics")
zonal_stats.SetParameterStringList("il", liste_chemin)
zonal_stats.SetParameterStringList("vec", [self.vector_used])
@@ -159,15 +154,15 @@ class Vector():
for idx, r in enumerate(resultats) :
self.stats_dict[idx] = r.tolist()
-
+
self.logger.info("End of stats 'mean' on {0}".format(os.path.split(self.vector_used)[1]))
def zonal_stats_pp(self, inraster):
"""
A zonal statistics ++ to dertermine pxl percent in every polygon
-
+
:param inraster: Input image path
- :type inraster: str
+ :type inraster: str
:returns: dict -- **p_stats** : dictionnary with pxl percent in every polygon. Mainly 'Maj_count' (Majority Value) and 'Maj_count_perc' (Majority Percent)
"""
@@ -191,30 +186,30 @@ class Vector():
dico['Maj_count'] = float(liste_item[1])
dico['Maj_count_perc'] = float(liste_item[2])
p_stats.append(dico)
-
+
return p_stats
-
+
def layer_rasterization(self, raster_head, attribute_r, **kwargs):
"""
Function to rasterize a vector using OTB.
-
+
@param raster_head: Raster path that will look like the final raster of the rasterization
@type raster_head: str
@param attribute_r: Field name of the shapefile that contains class names
@type attribute_r: str
- @kwargs: **choice_nb_b** (int) - Output image number of band. If you choice 1, take first band. If you choice 2, take two first band etc...
+ @kwargs: **choice_nb_b** (int) - Output image number of band. If you choice 1, take first band. If you choice 2, take two first band etc...
@returns: str -- **valid_raster** : output raster path from the rasterization
"""
valid_raster = "{0}.TIF".format(self.vector_used[:-4])# Name of the output raster
self.logger.debug("valid_raster : {0}".format(valid_raster))
-
+
if os.path.exists(valid_raster):
os.remove(valid_raster)
-
+
layerRasterization = otb.Registry.CreateApplication("Rasterization")
layerRasterization.SetParameterString("in", self.vector_used)
layerRasterization.SetParameterString("out", valid_raster)
@@ -223,5 +218,5 @@ class Vector():
layerRasterization.SetParameterString("mode.attribute.field", attribute_r)
layerRasterization.ExecuteAndWriteOutput()
-
- return valid_raster
\ No newline at end of file
+
+ return valid_raster
--
GitLab