physion 1.1__tar.gz → 1.2__tar.gz

{physion-1.1/src/physion.egg-info → physion-1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: physion
-Version: 1.1
+Version: 1.2
 Summary: Vision Physiology Software
 Author-email: Yann Zerlaut <yann.zerlaut@gmail.com>
 Project-URL: Homepage, https://github.com/yzerlaut/physion
@@ -29,9 +29,10 @@ Requires-Dist: ffmpeg-python
 Requires-Dist: pyqt5
 Requires-Dist: openpyxl
 
-<!-- ** Build Instructions ** -->
-<!--  python -m build  -->
+<!--             ** Build Instructions **              -->
+<!--  python -m build                                  -->
 <!--  python -m twine upload --repository pypi dist/*  -->
+<!--                                                   -->
 
 <div><img src="./docs/icons/physion.png" alt="physion logo" width="35%" align="right" style="margin-left: 10px"></div>
 
@@ -53,7 +54,13 @@ The different modules are detailed in the [documentation below](README.md#module
 
 ## Install
 
-Simply:
+Create a `"physion"` environment running `python 3.11`, with:
+
+```
+conda create -n "physion" python=3.11
+```
+
+Then simply:
 ```
 pip install physion
 ```

{physion-1.1 → physion-1.2}/README.md

@@ -1,6 +1,7 @@
-<!-- ** Build Instructions ** -->
-<!--  python -m build  -->
+<!--             ** Build Instructions **              -->
+<!--  python -m build                                  -->
 <!--  python -m twine upload --repository pypi dist/*  -->
+<!--                                                   -->
 
 <div><img src="./docs/icons/physion.png" alt="physion logo" width="35%" align="right" style="margin-left: 10px"></div>
 
@@ -22,7 +23,13 @@ The different modules are detailed in the [documentation below](README.md#module
 
 ## Install
 
-Simply:
+Create a `"physion"` environment running `python 3.11`, with:
+
+```
+conda create -n "physion" python=3.11
+```
+
+Then simply:
 ```
 pip install physion
 ```

{physion-1.1 → physion-1.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "physion"
-version = "1.1"
+version = "1.2"
 authors = [
   { name="Yann Zerlaut", email="yann.zerlaut@gmail.com" },
 ]

{physion-1.1 → physion-1.2}/src/physion/__main__.py

@@ -1,4 +1,4 @@
-import sys
+import sys, os
 from PyQt5 import QtWidgets
 
 from physion.gui.main import MainWindow
@@ -10,7 +10,11 @@ try:
 except ModuleNotFoundError:
     pass
 
-GUI = MainWindow(app)
+GUI = MainWindow(app,
+    filename=sys.argv[-1] if (('.nwb' in sys.argv[-1]) and \
+                    os.path.isfile(sys.argv[-1])) else None,
+    folder=sys.argv[-1] if ((len(sys.argv)>1) and \
+            os.path.isdir(sys.argv[-1])) else None)
 
 sys.exit(app.exec_())
 

physion-1.2/src/physion/acquisition/protocols/black-grey-white-20s-each-x5.json

@@ -0,0 +1,16 @@
+{
+  "Presentation": "Stimuli-Sequence",
+  "Stimulus": "uniform-bg",
+  "Screen": "Dell-2020",
+  "movie_refresh_freq":30,
+  "presentation-duration": 20,
+  "presentation-blank-screen-color": 0.5,
+  "presentation-prestim-period": 2,
+  "presentation-poststim-period": 2,
+  "presentation-interstim-period": 0,
+  "N-repeat": 5,
+  "starting-index": 0,
+  "bg-color-1": 0.0,
+  "bg-color-2": 1.0,
+  "N-bg-color": 3
+}

physion-1.2/src/physion/acquisition/protocols/injection-monitoring.json

@@ -0,0 +1,38 @@
+{
+  "Presentation": "Stimuli-Sequence",
+  "Stimulus": "center-grating",
+  "Screen": "Dell-2020",
+  "shuffling-seed": 1,
+  "movie_refresh_freq":30.0,
+  "units":"lin-deg",
+  "presentation-duration": 2,
+  "presentation-prestim-period": 10,
+  "presentation-poststim-period": 10,
+  "presentation-interstim-period": 8,
+  "presentation-blank-screen-color": 0.5,
+  "N-repeat": 38,
+  "angle-1": 0,
+  "angle-2": 157.5,
+  "N-angle": 8,
+  "spatial-freq-1": 0.04,
+  "spatial-freq-2": 0.04,
+  "N-spatial-freq": 0,
+  "radius-1": 200,
+  "radius-2": 200,
+  "N-radius": 0,
+  "x-center-1": 0.0,
+  "x-center-2": 0.0,
+  "N-x-center": 0,
+  "y-center-1": 0.0,
+  "y-center-2": 0.0,
+  "N-y-center": 0,
+  "contrast-1": 1.0,
+  "contrast-2": 1.0,
+  "N-contrast": 1,
+  "bg-color-1": 0.5,
+  "bg-color-2": 0.5,
+  "N-bg-color": 0,
+  "phase-1": 90.0,
+  "phase-2": 90.0,
+  "N-phase": 0
+}

{physion-1.1 → physion-1.2}/src/physion/acquisition/run.py

@@ -59,10 +59,7 @@ def init_VisualStim(self):
     p = self.protocol.copy() # a copy of the protocol data for saving
     p['no-window'] = True
     stim = build_VisualStim(p)
-    np.save(os.path.join(self.date_time_folder,
-            'visual-stim.npy'), stim.experiment)
-    print('[ok] Visual-stimulation data saved as "%s"' %\
-            os.path.join(self.date_time_folder, 'visual-stim.npy'))
+    stim.save(self.date_time_folder) # writes visual-stim.npy & protocol.json
 
     self.max_time = stim.experiment['time_stop'][-1]+\
             stim.experiment['time_start'][0]
@@ -148,7 +145,14 @@ def run(self):
 
         NIdaq_metadata_init(self)
 
-        if not self.onlyDemoButton.isChecked():
+        if self.onlyDemoButton.isChecked():
+            np.save(os.path.join(self.date_time_folder, 'NIdaq.start.npy'),
+                    time.time()*np.ones(1))
+            np.save(os.path.join(self.date_time_folder, 'NIdaq.npy'),
+                    {'analog':np.zeros((1,20000)),
+                     'digital':np.zeros((1,20000)),
+                     'dt':1e-2})
+        else:
             try:
                 self.acq = Acquisition(\
                     sampling_rate=\
@@ -164,6 +168,7 @@ def run(self):
                 print(e)
                 print('\n [!!] PB WITH NI-DAQ [!!] \n')
                 self.acq = None
+        
 
         # saving all metadata after full initialization:
         self.save_experiment(self.metadata) 

{physion-1.1 → physion-1.2}/src/physion/acquisition/tools.py

@@ -50,14 +50,6 @@ def save_experiment(self, metadata):
                          '%s.xlsx' % self.subjectBox.currentText()))
     print('[ok] Subject data saved as: %s.xlsx' % self.subjectBox.currentText())
 
-    # SAVING THE PROTOCOL FILE
-    if self.protocolBox.currentText()!='None':
-        shutil.copy(os.path.join(base_path, 'protocols',
-                                 self.protocolBox.currentText()+'.json'),
-                    filename.replace('metadata', 'protocol'))
-
-        print('[ok] Protocol data saved as: protocol.json ')
-
 
 
 def get_subject_props(self, filename=None):

physion-1.2/src/physion/analysis/__init__.py

@@ -0,0 +1,3 @@
+from . import stat_tools, tools, read_NWB, process_NWB, behavior, dataframe, protocols
+
+

{physion-1.1 → physion-1.2}/src/physion/analysis/read_NWB.py

@@ -502,7 +502,6 @@ class Data:
     ################################################
     
     def init_visual_stim(self, verbose=True):
-        self.metadata['load_from_protocol_data'], self.metadata['no-window'] = False, True
         self.metadata['verbose'] = verbose
         self.visual_stim = build_stim(self.metadata)
 
@@ -590,44 +589,73 @@ class Data:
         
     def list_subquantities(self, quantity):
         if quantity=='CaImaging':
-            return ['rawFluo', 'dFoF', 'neuropil', 'Deconvolved',
-                    'F-0.7*Fneu', 'F-Fneu', 'd(F-Fneu)', 'd(F-0.7*Fneu)']
+            return ['rawFluo', 'neuropil', 'dFoF', 'Deconvolved']
         else:
             return ['']
         
             
         
 def scan_folder_for_NWBfiles(folder, 
+                             for_protocol=None,
+                             for_protocols=[],
                              sorted_by='filename',
                              Nmax=1000000,
                              exclude_intrinsic_imaging_files=True,
                              verbose=True):
     """
-    scan folders for protocols and returns a A
+    scan folders for protocols and returns a list of datafiles
 
-    by default: exccludes the intrinsic imaging files
+    by default: excludes the intrinsic imaging files
     """
     if verbose:
         print('inspecting the folder "%s" [...]' % folder)
         t0 = time.time()
 
-    FILES = get_files_with_extension(folder,
+    if (for_protocol is not None) and (len(for_protocols)==0):
+        for_protocols = [for_protocol]
+
+    FILES0 = get_files_with_extension(folder,
                     extension='.nwb', recursive=True)
     
     if exclude_intrinsic_imaging_files:
-        FILES = [f for f in FILES if (('left-' not in f) and\
+        FILES0 = [f for f in FILES0 if (('left-' not in f) and\
                                       ('down-' not in f) and\
                                       ('right-' not in f) and\
                                       ('up-' not in f))]
 
-    DATES = np.array([f.split(os.path.sep)[-1].split('-')[0] for f in FILES])
-    SUBJECTS, PROTOCOLS = [], []
+    DATES = np.array([f.split(os.path.sep)[-1].split('-')[0] for f in FILES0])
+    FILES, SUBJECTS, PROTOCOLS, PROTOCOL_IDS = [], [], [], []
+
+    for f in FILES0[:Nmax]:
 
-    for f in FILES[:Nmax]:
         try:
             data = Data(f, metadata_only=True, verbose=False)
-            PROTOCOLS.append(data.protocols)
-            SUBJECTS.append(data.metadata['subject_ID'])
+
+            if len(for_protocols)>0:
+
+                # we look for specific protocols
+                iProtocols, Protocols = [], []
+                for protocol in for_protocols:
+                    iP = np.flatnonzero(data.protocols==protocol)
+                    if len(iP)==1:
+                        iProtocols.append(iP[0])
+                        Protocols.append(data.protocols[iP[0]])
+
+                if len(Protocols)>0:
+                    # if it has at least one protocol, we include it
+                    FILES.append(f)
+                    PROTOCOLS.append(Protocols)
+                    PROTOCOL_IDS.append(iProtocols)
+                    SUBJECTS.append(data.metadata['subject_ID'])
+
+            else:
+
+                # we include with all protocols
+                FILES.append(f)
+                PROTOCOLS.append(data.protocols)
+                PROTOCOL_IDS.append(range(len(data.protocols)))
+                SUBJECTS.append(data.metadata['subject_ID'])
+
         except BaseException as be:
             SUBJECTS.append('N/A')
             if verbose:
@@ -635,7 +663,8 @@ def scan_folder_for_NWBfiles(folder,
                 print('\n [!!] Pb with "%s" \n' % f)
         
     if verbose:
-        print(' -> found n=%i datafiles (in %.1fs) ' % (len(FILES), (time.time()-t0)))
+        print(' -> found n=%i datafiles (in %.1fs) ' % (len(FILES),
+                                                        (time.time()-t0)))
 
     # sorted by filename
 
@@ -652,4 +681,5 @@ def scan_folder_for_NWBfiles(folder,
     return {'files':np.array(FILES)[isorted], 
             'dates':np.array(DATES)[isorted],
             'subjects':np.array(SUBJECTS)[isorted],
+            'protocol_ids':[PROTOCOL_IDS[i] for i in isorted],
             'protocols':[PROTOCOLS[i] for i in isorted]}

{physion-1.1 → physion-1.2}/src/physion/assembling/add_ophys.py

@@ -11,11 +11,13 @@ sys.path.append(str(pathlib.Path(__file__).resolve().parents[2]))
 # import the 2P trigger delay from the acquisition module !
 from physion.acquisition.recordings.Scan1Plane_Screen342V import TwoP_trigger_delay
 
-from physion.assembling.IO.binary import BinaryFile
-from physion.assembling.IO.bruker_xml_parser import bruker_xml_parser
+from physion.imaging.bruker.xml_parser import bruker_xml_parser
+from physion.imaging.suite2p.to_nwb import add_ophys_processing_from_suite2p
+
 from physion.utils.files import get_files_with_extension, get_TSeries_folders
+from physion.utils.binary import BinaryFile
+
 from physion.assembling.tools import build_subsampling_from_freq
-from physion.assembling.IO.suite2p_to_nwb import add_ophys_processing_from_suite2p
 from physion.utils.paths import FOLDERS, python_path
 from physion.analysis.read_NWB import Data