physion 1.2__tar.gz → 1.2.1__tar.gz

{physion-1.2/src/physion.egg-info → physion-1.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: physion
-Version: 1.2
+Version: 1.2.1
 Summary: Vision Physiology Software
 Author-email: Yann Zerlaut <yann.zerlaut@gmail.com>
 Project-URL: Homepage, https://github.com/yzerlaut/physion
@@ -38,7 +38,7 @@ Requires-Dist: openpyxl
 
 # Vision Physiology Software
 
-> *An integrated software for cellular and network physiology of visual circuits in behaving mice*
+> *An integrated software for cellular and circuit physiology of visual processing during behavior*
 
 --------------------
 
@@ -65,14 +65,9 @@ Then simply:
 pip install physion
 ```
 
-**For an installation on an acquisition setup, see the detailed steps in [docs/install/README.md](./docs/install/README.md)**
+- For an installation on an acquisition setup, see the detailed steps in [./docs/install/acquisition.md](./docs/install/acquisition.md)
+- For some installation issues, see [./docs/install/troubleshooting.md](./docs/install/troubleshooting.md)
 
-#### troubleshooting
-
-- the `PyQt` package can be broken after those steps, re-start from a fresh install with `pip uninstall PyQt5` and `pip install PyQt5`. 
-- In linux, the `libqxcb.so` binding is making problems, this can be solved by deleting the following file: `rm ~/miniconda3/lib/python3.11/site-packages/cv2/qt/plugins/platforms/libqxcb.so`.
-- In linux, there can be a `krb5` version mismatch between Qt and Ubuntu packages. Download the latest on [the kerboeros website](https://web.mit.edu/kerberos/) and install it from source with: `tar xf krb5-1.18.2.tar.gz; cd krb5-1.18.2/src; ./configure --prefix=/opt/krb5/ ; make && sudo make install`. Then do the binding with: `export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/krb5/lib` (you can put this in your `~/.bashrc`).
- 
 ## Usage
 
 Run:

{physion-1.2 → physion-1.2.1}/README.md

@@ -7,7 +7,7 @@
 
 # Vision Physiology Software
 
-> *An integrated software for cellular and network physiology of visual circuits in behaving mice*
+> *An integrated software for cellular and circuit physiology of visual processing during behavior*
 
 --------------------
 
@@ -34,14 +34,9 @@ Then simply:
 pip install physion
 ```
 
-**For an installation on an acquisition setup, see the detailed steps in [docs/install/README.md](./docs/install/README.md)**
+- For an installation on an acquisition setup, see the detailed steps in [./docs/install/acquisition.md](./docs/install/acquisition.md)
+- For some installation issues, see [./docs/install/troubleshooting.md](./docs/install/troubleshooting.md)
 
-#### troubleshooting
-
-- the `PyQt` package can be broken after those steps, re-start from a fresh install with `pip uninstall PyQt5` and `pip install PyQt5`. 
-- In linux, the `libqxcb.so` binding is making problems, this can be solved by deleting the following file: `rm ~/miniconda3/lib/python3.11/site-packages/cv2/qt/plugins/platforms/libqxcb.so`.
-- In linux, there can be a `krb5` version mismatch between Qt and Ubuntu packages. Download the latest on [the kerboeros website](https://web.mit.edu/kerberos/) and install it from source with: `tar xf krb5-1.18.2.tar.gz; cd krb5-1.18.2/src; ./configure --prefix=/opt/krb5/ ; make && sudo make install`. Then do the binding with: `export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/krb5/lib` (you can put this in your `~/.bashrc`).
- 
 ## Usage
 
 Run:

{physion-1.2 → physion-1.2.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "physion"
-version = "1.2"
+version = "1.2.1"
 authors = [
   { name="Yann Zerlaut", email="yann.zerlaut@gmail.com" },
 ]

{physion-1.2 → physion-1.2.1}/src/physion/analysis/dataframe.py

@@ -41,7 +41,7 @@ def NWB_to_dataframe(nwbfile,
     if time_sampling_reference=='dFoF' and ('ophys' in data.nwbfile.processing):
         time = np.array(data.Fluorescence.timestamps[:])[::subsampling]
     else:
-        print('taking running pseed by default')
+        print('taking running speed by default')
         time = data.t_running_speed[::subsampling]
 
     dataframe = pandas.DataFrame({'time':time})
@@ -57,9 +57,9 @@ def NWB_to_dataframe(nwbfile,
                             interpolation='linear',
                             verbose=verbose)
 
-        dataframe.vNrois = data.vNrois
+        dataframe.nROIs = data.nROIs
 
-        for i in range(data.vNrois):
+        for i in range(data.nROIs):
 
             if ('dFoF' in normalize) or (normalize=='all'):
                 dataframe['dFoF-ROI%i'%i] = Normalize(data.dFoF[i,:])
@@ -258,8 +258,9 @@ def build_stim_specific_array(data, index_cond, time,
         if i<data.nwbfile.stimulus['time_start_realigned'].num_samples:
             tstart = data.nwbfile.stimulus['time_start_realigned'].data[i]
             tstop = data.nwbfile.stimulus['time_stop_realigned'].data[i]
+            
 
-            t_cond = (time>=tstart) & (time<tstop)
+            t_cond = (time>=float(tstart)) & (time<float(tstop))
             array[t_cond] = True
 
     # TO BE FIXED

{physion-1.2 → physion-1.2.1}/src/physion/analysis/process_NWB.py

@@ -17,6 +17,18 @@ class EpisodeData:
             the raw signal on a fixed time interval (surrounding the stim)
 
     - Using metadata to store stimulus informations per episode
+
+    quantities should be given as:
+            - Photodiode-Signal
+            - running_speed
+            - Deconvolved
+            - dFoF
+            - Zscore_dFoF
+            - neuropil
+            - rawFluo
+            - pupil_diameter
+            - gaze_movement
+            - facemotion
     """
 
     def __init__(self, full_data,
@@ -145,7 +157,7 @@ class EpisodeData:
                 full_data.nwbfile.stimulus['time_start'].data[self.protocol_cond_in_full_data,0][0]
         idur = int(duration/dt_sampling/1e-3)
         # -> time array:
-        self.t = np.arange(-ipre+1, idur+ipre-1)*dt_sampling*1e-3
+        self.t = np.arange(-ipre+2, idur+ipre)*dt_sampling*1e-3
 
 
         #############################################################################

{physion-1.2 → physion-1.2.1}/src/physion/assembling/nwb.py

@@ -26,15 +26,9 @@ ALL_MODALITIES = ['raw_CaImaging', 'processed_CaImaging',
                   'VisualStim',
                   'Locomotion'] 
 
-
-def build_NWB_func(args):
-    
-    if args.verbose:
-        print('- Initializing NWB file for "%s" [...]' % args.datafolder)
-
-    #################################################
-    ####            BASIC metadata            #######
-    #################################################
+def read_metadata(args):
+    """
+    """
 
     if os.path.isfile(os.path.join(args.datafolder, 'metadata.json')):
         with open(os.path.join(args.datafolder, 'metadata.json'),
@@ -45,6 +39,16 @@ def build_NWB_func(args):
         metadata = np.load(os.path.join(args.datafolder, 'metadata.npy'),
                            allow_pickle=True).item()
 
+    return metadata 
+
+def build_NWB_func(args):
+    """
+    """
+    if args.verbose:
+        print('- Initializing NWB file for "%s" [...]' % args.datafolder)
+
+    metadata = read_metadata(args)
+
     # add visual stimulation protocol parameters to the metadata:
     if os.path.isfile(os.path.join(args.datafolder, 'protocol.json')):
         with open(os.path.join(args.datafolder, 'protocol.json'),
@@ -84,7 +88,7 @@ def build_NWB_func(args):
             subject_file = [f for f in os.listdir(args.datafolder) if '.xlsx' in f][0]
             print('- Adding Subject data from the file: "%s" (TO BE DONE)' % subject_file)
         except BaseException:
-            print('[!!] / ! \\ no Subject .xlsx file found / ! \\ ')
+            print('     [!!] no Subject .xlsx file found [!!]   ')
 
     #################################
     # Implement READ from CSV here ##
@@ -319,19 +323,13 @@ def build_NWB_func(args):
 
         fcamData = CameraData('FaceCamera', folder=args.datafolder)
 
-        if os.path.isfile(os.path.join(args.datafolder, 'FaceCamera-summary.npy')):
-            FCS_data = np.load(os.path.join(args.datafolder, 'FaceCamera-summary.npy'),
-                               allow_pickle=True).item()
-            FC_times = FCS_data['times'] # can be overwritten later
-        else:
-            FCS_data = None
-
+        FC_times = fcamData.times
         FC_times = check_times(FC_times, NIdaq_Tstart)
 
-        if ('raw_FaceCamera' in args.modalities) and (fcamData is not None):
-            
-            FC_times = fcamData.times
-            FC_times = check_times(FC_times, NIdaq_Tstart)
+        if ('raw_FaceCamera' in args.modalities) and (len(fcamData.times)>0):
+           
+            FC_timesR = fcamData.times
+            FC_timesR = check_times(FC_timesR, NIdaq_Tstart)
 
             imgR = fcamData.get(0)
             FC_SUBSAMPLING = build_subsampling_from_freq(args.FaceCamera_frame_sampling,
@@ -352,30 +350,7 @@ def build_NWB_func(args):
             FaceCamera_frames = pynwb.image.ImageSeries(name='FaceCamera',
                                                         data=FC_dataI,
                                                         unit='NA',
-                                                        timestamps=FC_times[FC_SUBSAMPLING])
-            nwbfile.add_acquisition(FaceCamera_frames)
-                
-        elif ('raw_FaceCamera' in args.modalities) and (FCS_data is not None):
-
-            imgR = FCS_data['sample_frames'][0]
-            def FaceCamera_frame_generator():
-                for i in range(len(FCS_data['sample_frames'])):
-                    try:
-                        yield FCS_data['sample_frames'][i].astype(np.uint8).reshape(imgR.shape)
-                    except ValueError:
-                        print('Pb in FaceCamera with frame #', i)
-                        yield np.zeros(imgR.shape)[shape_cond]
-                        
-            FC_dataI = DataChunkIterator(data=FaceCamera_frame_generator(),
-                                         maxshape=(None, *imgR.shape),
-                                         dtype=np.dtype(np.uint8))
-            FaceCamera_frames = pynwb.image.ImageSeries(name='FaceCamera',
-                data=FC_dataI,
-                unit='NA',
-                timestamps=FC_times[np.linspace(0, len(FC_times)-1, 
-                                                len(FCS_data['sample_frames']), 
-                                                dtype=int)])
-                # timestamps=FC_times[FCS_data['sample_frames_index']]) # REPLACE THE ABOVE LINE AFTER SEPT 16th !!!
+                                                        timestamps=FC_timesR[FC_SUBSAMPLING])
             nwbfile.add_acquisition(FaceCamera_frames)
                 
         else:
@@ -396,6 +371,8 @@ def build_NWB_func(args):
                     
                 dataP = np.load(os.path.join(args.datafolder, 'pupil.npy'),
                                 allow_pickle=True).item()
+                print(len(FC_times))
+                print('pupil frames: ', len(dataP['frame']))
 
                 if 'FaceCamera-1cm-in-pix' in metadata:
                     pix_to_mm = 10./float(metadata['FaceCamera-1cm-in-pix']) # IN MILLIMETERS FROM HERE
@@ -418,7 +395,7 @@ def build_NWB_func(args):
                         pupil_module.add(PupilProp)
 
                 # then add the frames subsampled
-                if fcamData is not None:
+                if len(fcamData.times)>0:
                     imgP = fcamData.get(0)
                     x, y = np.meshgrid(np.arange(0,imgP.shape[0]), np.arange(0,imgP.shape[1]), indexing='ij')
                     cond = (x>=dataP['xmin']) & (x<=dataP['xmax']) & (y>=dataP['ymin']) & (y<=dataP['ymax'])
@@ -663,6 +640,12 @@ if __name__=='__main__':
     parser.add_argument('-sfs', "--FaceMotion_frame_sampling", default=0.005, type=float)
 
     parser.add_argument('-df', "--destination_folder", type=str, default='')
+    parser.add_argument('-op', "--only_protocol", type=str, default='',
+                        help="""
+                        In recursive mode,
+                        if you want to build files for a given protocol only
+                        e.g.: -oe drifting-gratings 
+                        """)
 
     parser.add_argument("--silent", action="store_true")
     parser.add_argument('-v', "--verbose", action="store_true")
@@ -687,7 +670,17 @@ if __name__=='__main__':
                 print(' processing "%s" [...] ' % f)
                 args.datafolder = f
                 args.filename = ''
-                build_NWB_func(args)
+                if args.only_protocol!='':
+                    # we check that it matches the protocol
+                    metadata = read_metadata(args)
+                    if args.only_protocol in metadata['protocol']:
+                        build_NWB_func(args)
+                    else:
+                        print('')
+                        print('  [!!]  ignoring:', f, ' of protocol', metadata['protocol'])
+                        print('')
+                else:
+                    build_NWB_func(args)
 
     elif os.path.isdir(args.datafolder) and (\
                 ('metadata.npy' in os.listdir(args.datafolder)) or

{physion-1.2 → physion-1.2.1}/src/physion/dataviz/raw.py

@@ -158,8 +158,8 @@ def add_VisualStim(data, tlim, ax,
 
     for i in np.arange(data.nwbfile.stimulus['time_start_realigned'].num_samples)[cond]:
 
-        tstart = data.nwbfile.stimulus['time_start_realigned'].data[i,0]
-        tstop = data.nwbfile.stimulus['time_stop_realigned'].data[i,0]
+        tstart = max([tlim[0], data.nwbfile.stimulus['time_start_realigned'].data[i,0]])
+        tstop = min([tlim[1], data.nwbfile.stimulus['time_stop_realigned'].data[i,0]])
         # ax.plot([tstart, tstop], [ylevel, ylevel], color=color)
         ax.fill_between([tstart, tstop], [0,0], np.zeros(2)+ylevel,
                         lw=0, alpha=0.05, color=color)

{physion-1.2 → physion-1.2.1}/src/physion/dataviz/tools.py

@@ -35,7 +35,8 @@ def plot_scaled_signal(data,
                        tlim, scale_bar,
                        scale_side='left',
                        ax_fraction_extent=1, ax_fraction_start=0,
-                       color='#1f77b4', scale_unit_string='%.1f'):
+                       color='#1f77b4', scale_unit_string='%.1f',
+                       lw=0.5):
     """
     # generic function to add scaled signal
     """
@@ -49,7 +50,7 @@ def plot_scaled_signal(data,
 
     ax.plot(t,
             ax_fraction_start+(signal-min_signal)*ax_fraction_extent/scale_range,
-            color=color, lw=1)
+            color=color, lw=lw)
 
     if scale_side=='left':
         tscale, side = shifted_start(tlim), 'right'

{physion-1.2 → physion-1.2.1}/src/physion/gui/main.py

@@ -85,7 +85,8 @@ class MainWindow(QtWidgets.QMainWindow):
         from physion.intrinsic.analysis import open_intrinsic_folder,\
                 moved_pixels, load_intrinsic_data, compute_phase_maps,\
                 compute_retinotopic_maps, perform_area_segmentation,\
-                update_img1, update_img2, save_intrinsic, pdf_intrinsic
+                update_img1, update_img2, save_intrinsic, pdf_intrinsic,\
+                reset_ROI
     else:
         from physion.gui.parts import inactivated as intrinsic
     # somatosensory
@@ -297,12 +298,11 @@ class MainWindow(QtWidgets.QMainWindow):
             # ---- DEBUG interface ---- #
             # self.SS_intrinsic()
             # self.facemotion()
-            self.pupil()
+            # self.pupil()
             # self.transfer_gui()
             # self.suite2p_preprocessing_UI()
             # self.build_NWB_UI()
             # self.add_imaging()
-            # self.intrinsic()
             # self.NWBs = ['/home/yann.zerlaut/DATA/JO-VIP-CB1/2022_11_16-15-17-59.nwb']
             # self.IMAGINGs = ['/home/yann.zerlaut/DATA/JO-VIP-CB1/Imaging-2Chan/TSeries-11162022-nomark-000']
             # self.runAddOphys()
@@ -314,6 +314,10 @@ class MainWindow(QtWidgets.QMainWindow):
             # self.trial_averaging()
             # self.FOV()
             # self.multimodal()
+            self.intrinsic()
+            self.lastBox.setChecked(False)
+            self.datafolder = '/Users/yann/UNPROCESSED/CIBELE/2024_06_28/14-35-30'
+            # self.load_intrinsic_data()
 
     def refresh(self):
         tab_id = self.tabWidget.currentIndex()

{physion-1.2 → physion-1.2.1}/src/physion/intrinsic/RetinotopicMapping.py

@@ -971,7 +971,11 @@ class RetinotopicMappingTrial(object):
     def __str__(self):
         return 'A retinotopic mapping trial: ' + self.getName()
 
-    def _getSignMap(self, isReverse=False, isPlot=False, isFixedRange=True):
+    def _getSignMap(self, 
+                    isReverse=False, 
+                    onlySMplot=False,
+                    isPlot=False, 
+                    isFixedRange=True):
 
         altPosMapf = ni.filters.gaussian_filter(self.altPosMap,
                                                 self.params['phaseMapFilterSigma'])
@@ -997,7 +1001,7 @@ class RetinotopicMappingTrial(object):
         signMapf = ni.filters.gaussian_filter(signMap,
                                               self.params['signMapFilterSigma'])
 
-        if isPlot:
+        if isPlot or onlySMplot:
             f1 = plt.figure(figsize=(7, 3.4))
             f1_231 = f1.add_subplot(231)
             if isFixedRange:
@@ -1048,6 +1052,7 @@ class RetinotopicMappingTrial(object):
             plt.axis('off')
             f1_236.set_title('sign map filtered')
 
+        if isPlot:
             f2 = plt.figure(figsize=(4, 1.4))
             f2_121 = f2.add_subplot(121)
             if altPowerMapf is not None:
@@ -1355,7 +1360,7 @@ class RetinotopicMappingTrial(object):
 
         return patches
 
-    def _mergePatches(self, isPlot=False):
+    def _mergePatches(self, isPlot=False, onlyPplot=False):
 
         if not hasattr(self, 'patchesAfterSplit'):
             self._splitPatches()
@@ -1494,7 +1499,7 @@ class RetinotopicMappingTrial(object):
 
         finalPatches = sortPatches(patches)
 
-        if isPlot:
+        if onlyPplot or isPlot:
             try:
                 zoom = self.vasculatureMap.shape[0] / self.altPosMap.shape[0]
             except:

{physion-1.2 → physion-1.2.1}/src/physion/intrinsic/analysis.py

@@ -9,6 +9,7 @@ from physion.utils.files import last_datafolder_in_dayfolder, day_folder
 from physion.intrinsic.tools import default_segmentation_params
 from physion.intrinsic import tools as intrinsic_analysis
 from physion.intrinsic import RetinotopicMapping
+from physion.pupil.roi import extract_ellipse_props, ellipse_props_to_ROI
 
 phase_color_map = pg.ColorMap(pos=np.linspace(0.0, 1.0, 3),
                               color=[(255, 0, 0),
@@ -38,7 +39,6 @@ def gui(self,
     self.datafolder, self.IMAGES = '', {} 
     self.subject, self.timestamps, self.data = '', '', None
 
-
     ##########################################################
     ####### GUI settings
     ##########################################################
@@ -85,7 +85,14 @@ def gui(self,
     self.add_side_widget(tab.layout,self.loadButton)
 
     # -------------------------------------------------------
-    self.add_side_widget(tab.layout,QtWidgets.QLabel(''))
+    # self.add_side_widget(tab.layout,QtWidgets.QLabel(''))
+
+    self.roiBox = QtWidgets.QCheckBox("ROI")
+    self.roiBox.setStyleSheet("color: gray;")
+    self.add_side_widget(tab.layout,self.roiBox, spec='small-middle')
+    self.roiButton = QtWidgets.QPushButton("reset", self)
+    self.roiButton.clicked.connect(self.reset_ROI)
+    self.add_side_widget(tab.layout,self.roiButton, 'small-right')
 
     self.pmButton = QtWidgets.QPushButton(\
             " == compute phase/power maps == ", self)
@@ -207,13 +214,16 @@ def gui(self,
                          self.nWidgetRow, 
                          self.nWidgetCol-self.side_wdgt_length)
 
-    self.raw_trace = self.graphics_layout.addPlot(row=0, col=0, rowspan=1, colspan=23)
+    self.raw_trace = self.graphics_layout.addPlot(row=0, col=0, 
+                                                  rowspan=1, colspan=23)
     
-    self.spectrum_power = self.graphics_layout.addPlot(row=1, col=0, rowspan=2, colspan=9)
+    self.spectrum_power = self.graphics_layout.addPlot(row=1, col=0, 
+                                                       rowspan=2, colspan=9)
     self.spDot = pg.ScatterPlotItem()
     self.spectrum_power.addItem(self.spDot)
     
-    self.spectrum_phase = self.graphics_layout.addPlot(row=1, col=9, rowspan=2, colspan=9)
+    self.spectrum_phase = self.graphics_layout.addPlot(row=1, col=9, 
+                                                       rowspan=2, colspan=9)
     self.sphDot = pg.ScatterPlotItem()
     self.spectrum_phase.addItem(self.sphDot)
 
@@ -239,18 +249,45 @@ def gui(self,
     self.graphics_layout.ci.layout.setRowStretchFactor(3, 5)
         
     # -------------------------------------------------------
-    self.pixROI = pg.ROI((0, 0), size=(10,10),
+    self.pixROI = pg.ROI((0, 0), size=(20,20),
                          pen=pg.mkPen((255,0,0,255)),
                          rotatable=False,resizable=False)
     self.pixROI.sigRegionChangeFinished.connect(self.moved_pixels)
     self.img1B.addItem(self.pixROI)
 
+    self.ROI = pg.EllipseROI([0, 0], [100, 100],
+                        movable = True,
+                        rotatable=False,
+                        resizable=True,
+                        pen= pg.mkPen((0, 0, 255), width=3,
+                                  style=QtCore.Qt.SolidLine),
+                        removable=True)
+    self.img1B.addItem(self.ROI)
+
     self.refresh_tab(tab)
 
     self.data = None
 
     self.show()
-    
+
+def reset_ROI(self):
+
+    if hasattr(self, 'ROI'):
+        self.ROI.sigRemoveRequested.connect(lambda: self.remove(self))
+        self.img1B.removeItem(self.ROI)
+
+    if 'raw-img-start' in self.IMAGES:
+        Ly, Lx = self.IMAGES['raw-img-start'].shape
+        self.ROI = pg.EllipseROI([0.05*Lx, 0.05*Ly], [0.9*Lx, 0.9*Ly],
+                            movable = True,
+                            rotatable=False,
+                            resizable=True,
+                            pen= pg.mkPen((0, 0, 255), width=3,
+                                      style=QtCore.Qt.SolidLine),
+                            removable=True)
+        self.img1B.addItem(self.ROI)
+
+
 def open_intrinsic_folder(self):
 
     self.datafolder = self.open_folder()
@@ -432,6 +469,11 @@ def show_raw_data(self):
 def compute_phase_maps(self):
 
     print('- computing phase maps [...]')
+    if self.roiBox.isChecked():
+        self.IMAGES['ROI'] = extract_ellipse_props(self.ROI)
+    else:
+        # a very large one
+        self.IMAGES['ROI'] = [-1000,-1000,20000,20000,0]
 
     intrinsic_analysis.compute_phase_power_maps(get_datafolder(self), 
                                                 self.protocolBox.currentText(),
@@ -533,12 +575,22 @@ def perform_area_segmentation(self):
         self.data['params'][key] = float(getattr(self, key+'Box').text())
 
     trial = RetinotopicMapping.RetinotopicMappingTrial(**self.data)
-    trial.processTrial(isPlot=True)
+    _ = trial._getSignMap(onlySMplot=True)
+    _ = trial._getRawPatchMap()
+    _ = trial._getRawPatches()
+    _ = trial._getDeterminantMap()
+    _ = trial._getEccentricityMap()
+    _ = trial._splitPatches()
+    _ = trial._mergePatches(onlyPplot=True)
+    intrinsic_analysis.plt.show()
     print(' -> area segmentation done ! ')
     
 
 def save_intrinsic(self):
 
+    # add ROI props
+    self.IMAGES['ROI_coords'] = ellipse_props_to_ROI(self.ROI)
+
     intrinsic_analysis.save_maps(self.IMAGES,
             os.path.join(self.datafolder, 'raw-maps.npy'))
     print('         current maps saved as: ', \

{physion-1.2 → physion-1.2.1}/src/physion/intrinsic/tools.py

@@ -9,6 +9,7 @@ from scipy.ndimage.filters import gaussian_filter1d, gaussian_filter
 from PIL import Image
 
 from physion.utils import plot_tools as pt
+from physion.pupil.process import inside_ellipse_cond, roi
 
 # from datavyz import graph_env
 ge_screen = None
@@ -203,6 +204,11 @@ def perform_fft_analysis(data, nrepeat,
 
     return rel_power, phase
 
+def find_ellipse_cond(maps, shape):
+    xc, yc, dx, dy, angle = maps['ROI']
+    x, y = np.meshgrid(np.arange(0, shape[0]),
+                       np.arange(0, shape[1]), indexing='ij')
+    return inside_ellipse_cond(x, y, yc, xc, dy, dx, -angle)
 
 def compute_phase_power_maps(datafolder, direction,
                              maps={},
@@ -214,13 +220,17 @@ def compute_phase_power_maps(datafolder, direction,
     if (p is None) or (t is None) or (data is None):
         p, (t, data) = load_raw_data(datafolder, direction, run_id=run_id)
 
-
     # FFT and write maps
     maps['%s-power' % direction],\
            maps['%s-phase' % direction] = perform_fft_analysis(data, p['Nrepeat'],
                                                     phase_range=phase_range)
     maps['%s-phase-range' % direction] = phase_range
 
+    if 'ROI' in maps:
+        ellipse = find_ellipse_cond(maps, (data.shape[1], data.shape[2]))
+        maps['%s-power' % direction][~ellipse] = 0
+        maps['%s-phase' % direction][~ellipse] = 0
+
     return maps
 
 def get_phase_to_angle_func(datafolder, direction):

{physion-1.2 → physion-1.2.1}/src/physion/pupil/process.py

@@ -184,7 +184,7 @@ def extract_boundaries_from_ellipse(ellipse, Lx, Ly):
     else:
         cx, cy, sx, sy = ellipse
         angle=0
-    x,y = np.meshgrid(np.arange(0,Lx), np.arange(0,Ly), indexing='ij')
+    x, y = np.meshgrid(np.arange(0,Lx), np.arange(0,Ly), indexing='ij')
     ellipse = inside_ellipse_cond(x, y, cx, cy, sx, sy, alpha=angle)
     xmin, xmax = np.min(x[ellipse]), np.max(x[ellipse])
     ymin, ymax = np.min(y[ellipse]), np.max(y[ellipse])