physion 1.2.1__tar.gz → 2.0__tar.gz

{physion-1.2.1/src/physion.egg-info → physion-2.0}/PKG-INFO

@@ -1,8 +1,8 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: physion
-Version: 1.2.1
+Version: 2.0
 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 +17,34 @@ 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: h5py
+Requires-Dist: hdmf
+Requires-Dist: pillow
+Requires-Dist: python-dateutil
+Requires-Dist: requests
+Provides-Extra: ephys
+Requires-Dist: open-ephys-python-tools>=1.0; extra == "ephys"
+Requires-Dist: spikeinterface[full]; extra == "ephys"
+Requires-Dist: probeinterface; extra == "ephys"
+Requires-Dist: elephant==1.0.0; extra == "ephys"
+Requires-Dist: neo==0.14.4; extra == "ephys"
+Provides-Extra: acquisition
+Requires-Dist: nidaqmx; extra == "acquisition"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Dynamic: license-file
 
 <!--             ** Build Instructions **              -->
 <!--  python -m build                                  -->
@@ -38,7 +55,7 @@ Requires-Dist: openpyxl
 
 # Vision Physiology Software
 
-> *An integrated software for cellular and circuit physiology of visual processing during behavior*
+> *An integrated software for the cellular and circuit physiology of visual processing during behavior*
 
 --------------------
 
@@ -60,9 +77,19 @@ 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
+```
+  with optional dependencies for electrophysiology (spike sorting, LFP, ephys notebooks) and/or for acquisition setups:
+```
+pip install "physion[ephys]"
+pip install "physion[ephys,acquisition]"
+```
+- 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/acquisition.md](./docs/install/acquisition.md)
@@ -86,7 +113,7 @@ 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)
@@ -101,3 +128,4 @@ 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-1.2.1 → physion-2.0}/README.md

@@ -7,7 +7,7 @@
 
 # Vision Physiology Software
 
-> *An integrated software for cellular and circuit physiology of visual processing during behavior*
+> *An integrated software for the cellular and circuit physiology of visual processing during behavior*
 
 --------------------
 
@@ -29,9 +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
+```
+  with optional dependencies for electrophysiology (spike sorting, LFP, ephys notebooks) and/or for acquisition setups:
+```
+pip install "physion[ephys]"
+pip install "physion[ephys,acquisition]"
+```
+- 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/acquisition.md](./docs/install/acquisition.md)
@@ -55,7 +65,7 @@ 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)
@@ -70,3 +80,4 @@ 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-2.0/pyproject.toml

@@ -0,0 +1,75 @@
+[project]
+name = "physion"
+version = "2.0"
+authors = [
+  { 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"
+requires-python = ">=3.9.5"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
+dependencies = [
+    "numpy",
+    "numba",
+    "scipy",
+    "matplotlib",
+    "scikit-image",
+    "scikit-learn",
+    "natsort",
+    "pynwb",
+    "pandas>=1.4.4",
+    "pyqt5.sip",
+    "pyqtgraph",
+    "pyqtdarktheme",
+    "opencv-python-headless",
+    "opencv-contrib-python-headless",
+    "ffmpeg-python",
+    "pyqt5",
+    "openpyxl",
+    # imported directly (previously only installed through other packages)
+    "h5py",
+    "hdmf",
+    "pillow",
+    "python-dateutil",
+    "requests",
+]
+
+[project.optional-dependencies]
+# electrophysiology: spike sorting, LFP, "Ephys-Analysis" and "CSD-Analysis" notebooks
+ephys = [
+    "open-ephys-python-tools>=1.0",
+    "spikeinterface[full]",
+    "probeinterface",
+    "elephant==1.0.0",
+    "neo==0.14.4",
+]
+# acquisition setups (camera SDKs: see docs/install/acquisition.md)
+acquisition = [
+    "nidaqmx",
+]
+test = ["pytest"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = ["test_*.py"]  # the other scripts of tests/ are not collected
+
+[tool.setuptools.packages.find]
+where = ["src"]
+[tool.setuptools.package-data]
+"physion.acquisition.protocols" = ["*.json"]
+"physion.acquisition.configs" = ["*.json"]
+"physion.acquisition" = ["DataTable.xlsx"]
+"physion.utils" = ["*.mplstyle"]
+"physion.visual_stim" = ["NI_bank/*.jpg"]
+
+[project.urls]
+"Homepage" = "https://github.com/yzerlaut/physion"
+"Documentation" = "https://github.com/yzerlaut/physion/README.md"
+"Bug Tracker" = "https://github.com/yzerlaut/physion/issues"
+

physion-2.0/src/physion/__init__.py

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

{physion-1.2.1 → physion-2.0}/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-2.0/src/physion/acquisition/__init__.py

@@ -0,0 +1,43 @@
+from . import settings, tools, run
+
+MODALITIES = ['NIDAQ',
+              'FaceCamera',
+              'RigCamera',
+              'ImagingCamera',
+              'Neuropixels',
+              'CaImaging',
+              'onlyDemo']
+
+EXPERIMENTERS = {
+    '':{'folder':''},
+    'Adrianna Nozownik':{
+        'folder':'Adrianna'
+        },
+    'Cibele Martins Pinho':{
+        'folder':'Cibele'
+        },
+    'Dhanasak Dhanasobhon':{
+        'folder':'Taddy'
+        },
+    'Joana Lourenco':{
+        'folder':'Joana'
+        },
+    'Laura Sofia Gonzalez':{
+        'folder':'Sofia'
+        },
+    'Nathan Mallet':{
+        'folder':'Nathan'
+        },
+    'Pan Sally Zhang':{
+        'folder':'Sally'
+        },
+    'Nelson Rebola':{
+        'folder':'Nelson'
+        },
+    'Valentin Ritou':{
+        'folder':'Valentin'
+        },
+    'Yann Zerlaut':{
+        'folder':'Yann'
+        },
+}

physion-2.0/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-1.2.1/src/physion/acquisition/configs/Yann-A1-2P.json → physion-2.0/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-2.0/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-2.0/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-2.0/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"
+}