physion 1.2__tar.gz → 1.2.2__tar.gz

{physion-1.2/src/physion.egg-info → physion-1.2.2}/PKG-INFO

@@ -1,8 +1,8 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: physion
-Version: 1.2
+Version: 1.2.2
 Summary: Vision Physiology Software
-Author-email: Yann Zerlaut <yann.zerlaut@gmail.com>
+Author-email: Yann Zerlaut <yann.zerlaut@icm-institute.org>, Mai-An Nguyen <mai-an.nguyen@icm-institute.org>, Laura Sofia Gonzalez <laura.gonzalez@icm-institute.org>
 Project-URL: Homepage, https://github.com/yzerlaut/physion
 Project-URL: Documentation, https://github.com/yzerlaut/physion/README.md
 Project-URL: Bug Tracker, https://github.com/yzerlaut/physion/issues
@@ -17,17 +17,24 @@ Requires-Dist: numba
 Requires-Dist: scipy
 Requires-Dist: matplotlib
 Requires-Dist: scikit-image
+Requires-Dist: scikit-learn
 Requires-Dist: natsort
 Requires-Dist: pynwb
 Requires-Dist: pandas>=1.4.4
 Requires-Dist: pyqt5.sip
 Requires-Dist: pyqtgraph
 Requires-Dist: pyqtdarktheme
-Requires-Dist: opencv-python
-Requires-Dist: opencv-contrib-python
+Requires-Dist: opencv-python-headless
+Requires-Dist: opencv-contrib-python-headless
 Requires-Dist: ffmpeg-python
 Requires-Dist: pyqt5
 Requires-Dist: openpyxl
+Requires-Dist: open-ephys-python-tools>=1.0
+Requires-Dist: spikeinterface[full]
+Requires-Dist: probeinterface
+Requires-Dist: elephant==1.0.0
+Requires-Dist: neo==0.14.4
+Dynamic: license-file
 
 <!--             ** Build Instructions **              -->
 <!--  python -m build                                  -->
@@ -38,7 +45,7 @@ Requires-Dist: openpyxl
 
 # Vision Physiology Software
 
-> *An integrated software for cellular and network physiology of visual circuits in behaving mice*
+> *An integrated software for the cellular and circuit physiology of visual processing during behavior*
 
 --------------------
 
@@ -60,19 +67,19 @@ Create a `"physion"` environment running `python 3.11`, with:
 conda create -n "physion" python=3.11
 ```
 
-Then simply:
+Then either install:
+- the [Pypi build](https://pypi.org/project/physion/) with:
 ```
 pip install physion
 ```
+- from source with:
+```
+git clone https://github.com/yzerlaut/physion --recurse-submodules
+```
 
-**For an installation on an acquisition setup, see the detailed steps in [docs/install/README.md](./docs/install/README.md)**
-
-#### troubleshooting
+- 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)
 
-- 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:
@@ -91,7 +98,7 @@ The different modules of the software are documented in the following links:
 - [Visual stimulation](src/physion/visual_stim/README.md)
 - [Multimodal Acquisition](src/physion/acquisition/README.md)
 - [Intrinsic Imaging](src/physion/intrinsic/README.md)
-- [Electrophysiology](src/physion/electrophy/README.md)
+- [Electrophysiology](src/physion/ephys/README.md)
 - [Calcium imaging](src/physion/imaging/README.md)
 - [Pupil tracking](src/physion/pupil/README.md)
 - [Face Motion tracking](src/physion/facemotion/README.md)
@@ -106,3 +113,4 @@ The different modules of the software are documented in the following links:
 ## Troubleshooting / Issues
 
 Use the dedicated [Issues](https://github.com/yzerlaut/physion/issues) interface of Github.
+

{physion-1.2 → physion-1.2.2}/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 the cellular and circuit physiology of visual processing during behavior*
 
 --------------------
 
@@ -29,19 +29,19 @@ Create a `"physion"` environment running `python 3.11`, with:
 conda create -n "physion" python=3.11
 ```
 
-Then simply:
+Then either install:
+- the [Pypi build](https://pypi.org/project/physion/) with:
 ```
 pip install physion
 ```
+- from source with:
+```
+git clone https://github.com/yzerlaut/physion --recurse-submodules
+```
 
-**For an installation on an acquisition setup, see the detailed steps in [docs/install/README.md](./docs/install/README.md)**
-
-#### troubleshooting
+- 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)
 
-- 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:
@@ -60,7 +60,7 @@ The different modules of the software are documented in the following links:
 - [Visual stimulation](src/physion/visual_stim/README.md)
 - [Multimodal Acquisition](src/physion/acquisition/README.md)
 - [Intrinsic Imaging](src/physion/intrinsic/README.md)
-- [Electrophysiology](src/physion/electrophy/README.md)
+- [Electrophysiology](src/physion/ephys/README.md)
 - [Calcium imaging](src/physion/imaging/README.md)
 - [Pupil tracking](src/physion/pupil/README.md)
 - [Face Motion tracking](src/physion/facemotion/README.md)
@@ -75,3 +75,4 @@ The different modules of the software are documented in the following links:
 ## Troubleshooting / Issues
 
 Use the dedicated [Issues](https://github.com/yzerlaut/physion/issues) interface of Github.
+

{physion-1.2 → physion-1.2.2}/pyproject.toml

@@ -1,8 +1,10 @@
 [project]
 name = "physion"
-version = "1.2"
+version = "1.2.2"
 authors = [
-  { name="Yann Zerlaut", email="yann.zerlaut@gmail.com" },
+  { name="Yann Zerlaut", email="yann.zerlaut@icm-institute.org" },
+  { name="Mai-An Nguyen", email="mai-an.nguyen@icm-institute.org" },
+  { name="Laura Sofia Gonzalez", email="laura.gonzalez@icm-institute.org" },
 ]
 description = "Vision Physiology Software"
 readme = "README.md"
@@ -18,17 +20,23 @@ dependencies = [
     "scipy",
     "matplotlib",
     "scikit-image",
+    "scikit-learn",
     "natsort",
     "pynwb",
     "pandas>=1.4.4",
     "pyqt5.sip",
     "pyqtgraph",
     "pyqtdarktheme",
-    "opencv-python",
-    "opencv-contrib-python",
+    "opencv-python-headless",
+    "opencv-contrib-python-headless",
     "ffmpeg-python",
     "pyqt5",
     "openpyxl",
+    "open-ephys-python-tools>=1.0",
+    "spikeinterface[full]",
+    "probeinterface",
+    "elephant==1.0.0",
+    "neo==0.14.4",
 ]
 
 [tool.setuptools.packages.find]
@@ -36,8 +44,7 @@ where = ["src"]
 [tool.setuptools.package-data]
 "physion.acquisition.protocols" = ["*.json"]
 "physion.acquisition.configs" = ["*.json"]
-"physion.acquisition.interventions" = ["*.json"]
-"physion.acquisition.subjects" = ["*.xlsx"]
+"physion.acquisition" = ["DataTable.xlsx"]
 
 [project.urls]
 "Homepage" = "https://github.com/yzerlaut/physion"

physion-1.2.2/src/physion/__init__.py

@@ -0,0 +1,3 @@
+from . import analysis, utils, dataviz, assembling, ephys,\
+        facemotion, gui, imaging, intrinsic, pupil, acquisition,\
+        visual_stim

{physion-1.2 → physion-1.2.2}/src/physion/__main__.py

@@ -1,6 +1,7 @@
-import sys, os
+import sys, os, time
 from PyQt5 import QtWidgets
 
+tic0 = time.time()
 from physion.gui.main import MainWindow
 app = QtWidgets.QApplication(sys.argv)
 
@@ -17,4 +18,5 @@ GUI = MainWindow(app,
             os.path.isdir(sys.argv[-1])) else None)
 
 sys.exit(app.exec_())
+print(' -> full init took: %.1fs' % (time.time()-tic0))
 

physion-1.2.2/src/physion/acquisition/__init__.py

@@ -0,0 +1,21 @@
+from . import settings, tools, run, recordings
+
+MODALITIES = ['NIDAQ',
+              'FaceCamera',
+              'RigCamera',
+              'ImagingCamera',
+              'Neuropixels',
+              'CaImaging',
+              'onlyDemo']
+
+EXPERIMENTERS = [
+    '',
+    'Adrianna Nozownik',
+    'Cibele Martins Pinho',
+    'Dhanasak Dhanasobhon',
+    'Joana Lourenco',
+    'Laura Sofia Gonzalez',
+    'Pan Sally Zhang',
+    'Valentin Ritou',
+    'Yann Zerlaut',
+]

physion-1.2.2/src/physion/acquisition/configs/Bacci-Neuropix.json

@@ -0,0 +1,65 @@
+{
+    "Rig":"Bacci-Neuropix", "physion-version":2.0,
+    "-----------------------------------------":"",
+    "Screen":"Dell-4220",
+    "-----------------------------------------":"",
+    "NIdaq":{
+        "acquisition-frequency":5000,
+        "analog-outputs":{
+            "N-channels":1,
+            "channel-labels":[
+                "trigger-for-2P-start"
+            ]
+        },
+        "analog-inputs":{
+            "N-channels":1,
+            "channel-labels":[
+                "photodiode-signal-from-screen"
+            ]
+        },
+        "digital-outputs":{
+            "lines":"port0/line0-3",
+            "line-labels":[
+                "ephys-synch-signal-irregular-5Hz",
+                "visual-stim-episode-start",
+                "LED-optogenetics-activation"
+            ]
+        },
+        "digital-inputs":{
+            "lines":"port0/line4-8",
+            "line-labels":[
+                "locomotion-channel1",
+                "locomotion-channel2",
+                "copy-ephys-synch-signal-irregular-5Hz",
+                "copy-visual-stim-episode-start",
+                "copy-LED-optogenetics-activation"
+            ]
+        }
+    },
+    "-----------------------------------------":"",
+    "FaceCamera":{
+        "frame-rate":30,
+        "1cm-in-pix":480
+    },
+    "-----------------------------------------":"",
+    "RigCamera":{
+        "frame-rate":20,
+        "1cm-in-pix":33
+    },
+    "-----------------------------------------":"",
+    "ImagingCamera":{
+        "frame-rate":20,
+        "1cm-in-pix":33
+    },
+    "Height-of-Microscope-Camera-Image-in-mm":2.7,
+    "-----------------------------------------":"",
+    "linear-treadmill":{
+        "radius-position-on-disk-cm":5.5,
+		"roto-encoder-value-per-rotation": -12563.0
+    },
+    "-----------------------------------------":"",
+    "root_datafolder":"DATA",
+    "lab":"Rebola and Bacci labs",
+    "institution":"Institut du Cerveau et de la Moelle, Paris",
+    "protocols":"all"
+}

physion-1.2/src/physion/acquisition/configs/Yann-A1-2P.json → physion-1.2.2/src/physion/acquisition/configs/Laptop+Lilliput.json

@@ -2,8 +2,8 @@
     "NIdaq-acquisition-frequency":10000,
     "NIdaq-analog-input-channels":1,
     "NIdaq-digital-input-channels":2,
-    "Rig":"ICM-A1-2P-setup",
-    "Screen":"Dell-2020",
+    "Rig":"Laptop+Microscope",
+    "Screen":"Lilliput",
     "Z-sign-correction-for-rig":-1,
     "FaceCamera-frame-rate":30,
     "FaceCamera-1cm-in-pix":480,

physion-1.2.2/src/physion/acquisition/configs/NIdaq-usage.json

@@ -0,0 +1,71 @@
+{
+    "Rig":"Test", "physion-version":2.0,
+    "-----------------------------------------":"",
+    "Screen":"Dell-2020",
+    "-----------------------------------------":"",
+    "NIdaq":{
+        "acquisition-frequency":1000,
+        "analog-outputs":{
+            "N-channels":2,
+            "channel-labels":[
+                "trigger-delay-1s",
+                "square-wave-TTL-1Hz"
+            ]
+        },
+        "analog-inputs":{
+            "N-channels":4,
+            "channel-labels":[
+                "chan1",
+                "chan2",
+                "chan3",
+                "chan4"
+            ]
+        },
+        "digital-outputs":{
+            "lines":"port0/line0:2",
+            "line-labels":[
+                "trigger-for-2P-start",
+                "visual-stim-episode-start",
+                ""
+            ]
+        },
+        "digital-inputs":{
+            "lines":"port0/line3:7",
+            "line-labels":[
+                "locomotion-channel1",
+                "locomotion-channel2",
+                "copy-visual-stim-start",
+                "",
+                ""
+            ]
+        }
+    },
+    "-----------------------------------------":"",
+    "FaceCamera":{
+        "frame-rate":30,
+        "1cm-in-pix":480
+    },
+    "-----------------------------------------":"",
+    "RigCamera":{
+        "frame-rate":20,
+        "1cm-in-pix":33
+    },
+    "-----------------------------------------":"",
+    "ImagingCamera":{
+        "frame-rate":20,
+        "1cm-in-pix":33
+    },
+    "Height-of-Microscope-Camera-Image-in-mm":2.7,
+    "-----------------------------------------":"",
+    "rotating-disk":{
+        "radius-position-on-disk-cm":5.5,
+		"roto-encoder-value-per-rotation": -12563.0
+    },
+    "-----------------------------------------":"",
+    "default-modalities":["NIDAQ"],
+    "-----------------------------------------":"",
+    "root_datafolder":"DATA",
+    "lab":"Rebola and Bacci labs",
+    "institution":"Institut du Cerveau et de la Moelle, Paris",
+    "protocols":"all"
+}

physion-1.2.2/src/physion/acquisition/configs/Rebol-A1-2P.json

@@ -0,0 +1,77 @@
+{
+    "Rig":"ICM-A1-2P-setup", "physion-version":2.0,
+    "-----------------------------------------":"",
+    "Screen":"Dell-2020",
+    "-----------------------------------------":"",
+    "NIdaq":{
+        "acquisition-frequency":5000,
+        "analog-outputs":{
+            "N-channels":0
+        },
+        "analog-inputs":{
+            "N-channels":1,
+            "channel-labels":[
+                "photodiode-signal-from-screen"
+            ]
+        },
+        "digital-outputs":{
+            "lines":"port0/line0:2",
+            "line-labels":[
+                "2P-start-stop-trigger-with-0.1s-delay",
+                "visual-stim-episode-start",
+                "LED-optogenetics-activation"
+            ]
+        },
+        "digital-inputs":{
+            "lines":"port0/line3:7",
+            "line-labels":[
+                "locomotion-channel1",
+                "locomotion-channel2",
+                "copy-visual-stim-episode-start",
+                "copy-LED-optogenetics-activation",
+                "copy-2P-start-stop-trigger"
+            ]
+        }
+    },
+    "-----------------------------------------":"",
+    "FaceCamera":{
+        "frame-rate":30,
+        "1cm-in-pix":480
+    },
+    "-----------------------------------------":"",
+    "RigCamera":{
+        "frame-rate":20,
+        "1cm-in-pix":33
+    },
+    "-----------------------------------------":"",
+    "ImagingCamera":{
+        "frame-rate":20,
+        "1cm-in-pix":33
+    },
+    "Height-of-Microscope-Camera-Image-in-mm":2.7,
+    "-----------------------------------------":"",
+    "LED":{
+        "wavelength":455.0,
+        "description":"TTL-controlled LED-driver",
+        "manufacturer":"Thorlabs", 
+        "fiber-location": "VIS"
+    },
+    "-----------------------------------------":"",
+    "rotating-disk":{
+        "radius-position-on-disk-cm":9.0,
+        "roto-encoder-value-per-rotation": -25300.0
+    },
+    "-----------------------------------------":"",
+    "2P":{
+        "Z-sign-correction-for-rig":-1, 
+        "onset-delay":0.1, 
+        "offset-advance":0.2},
+    "-----------------------------------------":"",
+    "default-modalities":["NIDAQ", 
+                          "CaImaging"],
+    "-----------------------------------------":"",
+    "root_datafolder":"DATA",
+    "lab":"Rebola and Bacci labs",
+    "institution":"Institut du Cerveau et de la Moelle, Paris",
+    "protocols":"all"
+}

physion-1.2.2/src/physion/acquisition/configs/Rebol-Neuropix.json

@@ -0,0 +1,71 @@
+{
+    "Rig":"Neuropix-LN-U3screens", "physion-version":2.0,
+    "-----------------------------------------":"",
+    "Screen":"LN-VR-3screens",
+    "-----------------------------------------":"",
+    "NIdaq":{
+        "acquisition-frequency":5000,
+        "analog-outputs":{
+            "N-channels":0
+        },
+        "analog-inputs":{
+            "N-channels":1,
+            "channel-labels":[
+                "photodiode-signal-from-screen"
+            ]
+        },
+        "digital-outputs":{
+            "lines":"port0/line0:2",
+            "line-labels":[
+                "ephys-synch-signal-2Hz",
+                "visual-stim-episode-start",
+                "LED-optogenetics-activation"
+            ]
+        },
+        "digital-inputs":{
+            "lines":"port0/line3:7",
+            "line-labels":[
+                "copy-ephys-synch-signal",
+                "locomotion-channel1",
+                "locomotion-channel2",
+                "copy-visual-stim-episode-start",
+                "copy-LED-optogenetics-activation"
+            ]
+        }
+    },
+    "-----------------------------------------":"",
+    "FaceCamera":{
+        "frame-rate":30,
+        "1cm-in-pix":480
+    },
+    "-----------------------------------------":"",
+    "RigCamera":{
+        "frame-rate":20,
+        "1cm-in-pix":33
+    },
+    "-----------------------------------------":"",
+    "ImagingCamera":{
+        "frame-rate":20,
+        "1cm-in-pix":33
+    },
+    "Height-of-Microscope-Camera-Image-in-mm":2.7,
+    "-----------------------------------------":"",
+    "LED":{
+        "wavelength":455.0,
+        "description":"TTL-controlled LED-driver",
+        "manufacturer":"Thorlabs",
+        "fiber-location": "VIS"
+    },
+    "-----------------------------------------":"",
+    "treadmill":{
+        "radius-position-on-disk-cm":5
+    },
+    "-----------------------------------------":"",
+    "default-modalities":["NIDAQ",  
+                          "Neuropixels"],
+    "-----------------------------------------":"",
+    "root_datafolder":"DATA",
+    "lab":"Rebola and Bacci labs",
+    "institution":"Institut du Cerveau et de la Moelle, Paris",
+    "protocols":"all"
+}