Fix full-waveform save in csv or in zip

dev/test_mb_2023_4_mux_2023.py

@@ -85,10 +85,10 @@ if within_ohmpi:
     print('Starting test with OhmPi.')
     k = OhmPi()
     # k.get_data()
-    # k.load_sequence(os.path.join(os.path.dirname(__file__), '../sequences/wenner16.txt'))
-    # k.reset_mux()
+    k.load_sequence(os.path.join(os.path.dirname(__file__), '../sequences/wenner16.txt'))
+    k.reset_mux()
     # k.run_multiple_sequences(sequence_delay=20, nb_meas=3)
-    # k.run_sequence(injection_duration=0.2)
+    k.run_sequence(injection_duration=0.2)
     # k.rs_check(tx_volt=4)
     # k.test_mux(mux_id=None, activation_time=0.2)
     # k._hw.switch_mux([A, B, M, N], state='on')

doc/build/_sources/source_rst/api.rst.txt

@@ -7,6 +7,7 @@ API reference
 .. automodule:: ohmpi.ohmpi
    :members:
    
-
+.. automodule:: ohmpi.hardware_system
+   :members:
 
 

doc/build/genindex.html

@@ -141,6 +141,8 @@
     module
 
       <ul>
+        <li><a href="source_rst/api.html#module-ohmpi.hardware_system">ohmpi.hardware_system</a>
+</li>
         <li><a href="source_rst/api.html#module-ohmpi.ohmpi">ohmpi.ohmpi</a>
 </li>
       </ul></li>
@@ -152,6 +154,13 @@
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="source_rst/api.html#ohmpi.ohmpi.OhmPi">OhmPi (class in ohmpi.ohmpi)</a>
 </li>
+      <li>
+    ohmpi.hardware_system
+
+      <ul>
+        <li><a href="source_rst/api.html#module-ohmpi.hardware_system">module</a>
+</li>
+      </ul></li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li>

doc/build/py-modindex.html

@@ -96,6 +96,11 @@
        <td>
        <code class="xref">ohmpi</code></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="source_rst/api.html#module-ohmpi.hardware_system"><code class="xref">ohmpi.hardware_system</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;

doc/build/source_rst/api.html

@@ -646,7 +646,7 @@ Parameters can be:
 
 </dd></dl>
 
-</section>
+<span class="target" id="module-ohmpi.hardware_system"></span></section>
 
 
            </div>

doc/source/source_rst/api.rst

@@ -8,5 +8,3 @@ API reference
    :members:
    
 
-
-

ohmpi/config.py

@@ -21,57 +21,38 @@ r_shunt = 2.
 HARDWARE_CONFIG = {
     'ctl': {'model': 'raspberry_pi'},
     'pwr': {'model': 'pwr_batt', 'voltage': 12., 'interface_name': 'none'},
-    'tx':  {'model': 'mb_2023_0_X',
+    'tx':  {'model': 'mb_2024_0_2',
              'voltage_max': 50.,  # Maximum voltage supported by the TX board [V]
              'current_max': 4.80/(50*r_shunt),  # Maximum voltage read by the current ADC on the TX board [A]
              'r_shunt': r_shunt,  # Shunt resistance in Ohms
              'interface_name': 'i2c'
             },
-    'rx':  {'model': 'mb_2023_0_X',
-            'coef_p2': 2.50,  # slope for conversion for ADS, measurement in V/V
-            'sampling_rate': 50.,  # number of samples per second
-            'interface_name': 'i2c',
+    'rx':  {'model': 'mb_2024_0_2',
+             'latency': 0.010,  # latency in seconds in continuous mode
+             'sampling_rate': 50,  # number of samples per second
+             'interface_name': 'i2c'
             },
-    'mux':  # default properties given in config are system properties that will be
-            # overwritten by properties defined in each the board dict below.
-            # if defined in board specs, values out of specs will be bounded to remain in specs
-            # omitted properties in config will be set to board specs default values if they exist
-            {'boards':
-                {'mux_A':
-                     {'model': 'mux_2023_0_X',
-                      'mux_tca_address': 0x70,
-                      'roles': {'A': 'X'},
-                      'cabling': {(i, j): ('mux_A', i) for j in ['A'] for i in range(1, 65)},
-                      'voltage_max': 12.},
-                 'mux_B':
-                     {'model': 'mux_2023_0_X',
-                      'mux_tca_address': 0x71,
-                      'roles': {'B': 'X'},
-                      'cabling': {(i, j): ('mux_B', i) for j in ['B'] for i in range(1, 65)},
-                      'voltage_max': 12.},
-                 'mux_M':
-                     {'model': 'mux_2023_0_X',
-                      'mux_tca_address': 0x72,
-                      'roles': {'M': 'X'},
-                      'cabling': {(i, j): ('mux_M', i) for j in ['M'] for i in range(1, 65)},
-                      'voltage_max': 12.},
-                'mux_N':
-                     {'model': 'mux_2023_0_X',
-                      'mux_tca_address': 0x73,
-                      'roles': {'N': 'X'},
-                      'cabling': {(i, j): ('mux_N', i) for j in ['N'] for i in range(1, 65)},
-                      'voltage_max': 12.},
+    'mux': {'boards':
+                {'mux_00':
+                     {'model': 'mux_2024_0_X',
+                      'tca_address': None,
+                      'tca_channel': 0,
+                      'addr2': 'down',
+                      'addr1': 'down',
+                      'roles': {'A': 'X', 'B': 'Y', 'M': 'XX', 'N': 'YY'},
+                      'cabling': {(i+0, j): ('mux_00', i) for j in ['A', 'B', 'M', 'N'] for i in range(1, 9)},
+                      'voltage_max': 12.}
                  },
-             'default': {'interface_name': 'i2c',
-                         'voltage_max': 12.,
+             'default': {'interface_name': 'i2c_ext',
+                         'voltage_max': 100.,
                          'current_max': 3.}
-             }
-}
+            }
+    }
 
 # SET THE LOGGING LEVELS, MQTT BROKERS AND MQTT OPTIONS ACCORDING TO YOUR NEEDS
 # Execution logging configuration
 EXEC_LOGGING_CONFIG = {
-    'logging_level': logging.INFO,  # TODO: set logging level back to INFO
+    'logging_level': logging.INFO,
     'log_file_logging_level': logging.DEBUG,
     'logging_to_console': True,
     'file_name': f'exec{logging_suffix}.log',
@@ -95,8 +76,8 @@ DATA_LOGGING_CONFIG = {
 # State of Health logging configuration (For a future release)
 SOH_LOGGING_CONFIG = {
     'logging_level': logging.INFO,
-    'logging_to_console': True,
     'log_file_logging_level': logging.DEBUG,
+    'logging_to_console': True,
     'file_name': f'soh{logging_suffix}.log',
     'max_bytes': 16777216,
     'backup_count': 1024,

ohmpi/ohmpi.py

@@ -82,7 +82,8 @@ class OhmPi(object):
         self.update_settings(os.path.join(os.path.split(os.path.dirname(__file__))[0],'settings/default.json'))
 
         # read in acquisition settings
-        self.update_settings(settings)
+        if settings is not None:
+            self.update_settings(settings)
         self.exec_logger.debug('Initialized with settings:' + str(self.settings))
 
         # read quadrupole sequence
@@ -189,7 +190,7 @@ class OhmPi(object):
             fw_filename = filename.replace('.csv', '_fw.csv')
             if not os.path.exists(fw_filename):  # new file, write headers first
                 with open(fw_filename, 'w') as f:
-                    f.write('A,B,M,N,t,pulse,polarity,current,voltage\n')
+                    f.write('A,B,M,N,t,current,voltage\n')
             # write full data
             with open(fw_filename, 'a') as f:
                 dd = last_measurement['full_waveform']
@@ -198,7 +199,7 @@ class OhmPi(object):
                 mm = np.repeat(last_measurement['M'], dd.shape[0])
                 nn = np.repeat(last_measurement['N'], dd.shape[0])
                 fwdata = np.c_[aa, bb, mm, nn, dd]
-                np.savetxt(f, fwdata, fmt=['%d', '%d', '%d', '%d', '%.3f', '%.3f', '%.3f'])
+                np.savetxt(f, fwdata, delimiter=',', fmt=['%d', '%d', '%d', '%d', '%.3f', '%.3f', '%.3f'])
 
         if fw_in_csv:
             d = last_measurement['full_waveform']
@@ -712,42 +713,48 @@ class OhmPi(object):
 
         # file management
         if fw_in_csv:  # make sure we have the same number of columns
-            with open(filename, '.csv', 'r') as f:
+            with open(filename, 'r') as f:
                 x = f.readlines()
 
             # get column of start of full-waveform
             icol = 0
             for i, col in enumerate(x[0].split(',')):
-                if col == 't1':
+                if col == 'i0':
                     icol = i
                     break
 
             # get longest possible line
             max_length = np.max([len(row.split(',')) for row in x]) - icol
-            nreadings = max_length // 5
-            print('-----', nreadings, max_length)
+            nreadings = max_length // 3
 
             # create padding array for full-waveform  # TODO test this!
-            with open(filename, '.csv', 'w') as f:
+            with open(filename, 'w') as f:
                 # write back headers
                 xs = x[0].split(',')
                 f.write(','.join(xs[:icol]))
-                for col in ['t','s','p','v','i']:
-                    f.write(','.join([col + str(j+1) for j in range(nreadings)]))
-                f.write('\n')
+                f.write(',')
+                for i, col in enumerate(['t', 'i','v']):
+                    f.write(','.join([col + str(j) for j in range(nreadings)]))
+                    if col == 'v':
+                        f.write('\n')
+                    else:
+                        f.write(',')
+                # write back rows
                 for i, row in enumerate(x[1:]):
                     xs = row.split(',')
                     f.write(','.join(xs[:icol]))
+                    f.write(',')
                     fw = np.array(xs[icol:])
-                    fw_pad = fw.reshape((5, -1))
-                    fw_padded = np.zeros((max_length, 5))
+                    fw_pad = fw.reshape((3, -1)).T
+                    fw_padded = np.zeros((nreadings, 3), dtype=fw_pad.dtype)
                     fw_padded[:fw_pad.shape[0], :] = fw_pad
-                    f.write(','.join(fw_padded.flatten()) + '\n')
+                    f.write(','.join(fw_padded.T.flatten()).replace('\n', '') + '\n')
 
         if fw_in_zip:
-            with ZipFile(filename.replace('.csv', '_fw.zip'), 'w') as myzip:
-                myzip.write(filename.replace('.csv', '_fw.csv'))
-            os.remove(filename.replace('.csv', '_fw.csv'))
+            fwfilename = filename.replace('.csv', '_fw')
+            with ZipFile(fwfilename + '.zip', 'w') as myzip:
+                myzip.write(fwfilename + '.csv', os.path.basename(fwfilename) + '.csv')
+            os.remove(fwfilename + '.csv')
 
         # reset to idle if we didn't interrupt the sequence
         if self.status != 'stopping':

settings/default.json

@@ -7,7 +7,7 @@
     "tx_volt": 5,
     "duty_cycle": 0.5,
     "strategy": "constant",
-    "fw_in_csv": false,
+    "fw_in_csv": true,
     "fw_in_zip": true,
     "export_path": "data/measurements.csv"
 }
\ No newline at end of file