physion 1.0__tar.gz → 1.2__tar.gz

{physion-1.0/src/physion.egg-info → physion-1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: physion
-Version: 1.0
+Version: 1.2
 Summary: Vision Physiology Software
 Author-email: Yann Zerlaut <yann.zerlaut@gmail.com>
 Project-URL: Homepage, https://github.com/yzerlaut/physion
@@ -23,10 +23,16 @@ Requires-Dist: pandas>=1.4.4
 Requires-Dist: pyqt5.sip
 Requires-Dist: pyqtgraph
 Requires-Dist: pyqtdarktheme
-Requires-Dist: opencv-python-headless
+Requires-Dist: opencv-python
+Requires-Dist: opencv-contrib-python
+Requires-Dist: ffmpeg-python
 Requires-Dist: pyqt5
+Requires-Dist: openpyxl
 
-<!--<div><img src="https://github.com/yzerlaut/physion/raw/master/docs/physion.png" alt="physion logo" width="35%" align="right" style="margin-left: 10px"></div>-->
+<!--             ** 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>
 
@@ -48,15 +54,25 @@ The different modules are detailed in the [documentation below](README.md#module
 
 ## Install
 
-Simply:
+Create a `"physion"` environment running `python 3.11`, with:
+
 ```
-pip install physion
+conda create -n "physion" python=3.11
 ```
 
-N.B. the `PyQt` package can be broken after those steps, re-start from a fresh install with `pip uninstall PyQt5` and `pip install PyQt5`.
+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)**
 
+#### 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:
@@ -84,7 +100,8 @@ The different modules of the software are documented in the following links:
 - [Hardware control](src/physion/hardware/README.md)
 - [Visualization](src/physion/dataviz/README.md)
 - [Analysis](src/physion/analysis/README.md)
-- [Sharing](src/physion/sharing/README.md)
+- [Data Management](src/physion/utils/management/README.md)
+- [Data Sharing](src/physion/utils/sharing/README.md)
 
 ## Troubleshooting / Issues
 

{physion-1.0 → physion-1.2}/README.md

@@ -1,4 +1,7 @@
-<!--<div><img src="https://github.com/yzerlaut/physion/raw/master/docs/physion.png" alt="physion logo" width="35%" align="right" style="margin-left: 10px"></div>-->
+<!--             ** 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>
 
@@ -20,15 +23,25 @@ The different modules are detailed in the [documentation below](README.md#module
 
 ## Install
 
-Simply:
+Create a `"physion"` environment running `python 3.11`, with:
+
 ```
-pip install physion
+conda create -n "physion" python=3.11
 ```
 
-N.B. the `PyQt` package can be broken after those steps, re-start from a fresh install with `pip uninstall PyQt5` and `pip install PyQt5`.
+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)**
 
+#### 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:
@@ -56,7 +69,8 @@ The different modules of the software are documented in the following links:
 - [Hardware control](src/physion/hardware/README.md)
 - [Visualization](src/physion/dataviz/README.md)
 - [Analysis](src/physion/analysis/README.md)
-- [Sharing](src/physion/sharing/README.md)
+- [Data Management](src/physion/utils/management/README.md)
+- [Data Sharing](src/physion/utils/sharing/README.md)
 
 ## Troubleshooting / Issues
 

{physion-1.0 → physion-1.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "physion"
-version = "1.0"
+version = "1.2"
 authors = [
   { name="Yann Zerlaut", email="yann.zerlaut@gmail.com" },
 ]
@@ -24,8 +24,11 @@ dependencies = [
     "pyqt5.sip",
     "pyqtgraph",
     "pyqtdarktheme",
-    "opencv-python-headless",
+    "opencv-python",
+    "opencv-contrib-python",
+    "ffmpeg-python",
     "pyqt5",
+    "openpyxl",
 ]
 
 [tool.setuptools.packages.find]
@@ -34,7 +37,7 @@ where = ["src"]
 "physion.acquisition.protocols" = ["*.json"]
 "physion.acquisition.configs" = ["*.json"]
 "physion.acquisition.interventions" = ["*.json"]
-"physion.acquisition.subjects" = ["*.csv"]
+"physion.acquisition.subjects" = ["*.xlsx"]
 
 [project.urls]
 "Homepage" = "https://github.com/yzerlaut/physion"

physion-1.2/src/physion/__init__.py

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

{physion-1.0 → physion-1.2}/src/physion/__main__.py

@@ -1,17 +1,20 @@
-import sys
+import sys, os
 from PyQt5 import QtWidgets
 
 from physion.gui.main import MainWindow
 app = QtWidgets.QApplication(sys.argv)
 
-
 try:
     import qdarktheme # pip install pyqtdarktheme
     app.setStyleSheet(qdarktheme.load_stylesheet('dark'))
 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/__init__.py

@@ -0,0 +1,10 @@
+from . import settings, tools, run, recordings
+
+MODALITIES = ['Locomotion',
+              'FaceCamera',
+              'RigCamera',
+              # 'EphysLFP',
+              # 'EphysVm',
+              'Neuropixels',
+              'CaImaging',
+              'onlyDemo']

physion-1.2/src/physion/acquisition/configs/Adrianna-Bacci-2P.json

@@ -0,0 +1,21 @@
+{
+    "NIdaq-acquisition-frequency":10000,
+    "NIdaq-analog-input-channels":1,
+    "NIdaq-digital-input-channels":2,
+    "Rig":"Bacci-2P-setup",
+    "Screen":"Dell-2020",
+    "Z-sign-correction-for-rig":1,
+    "FaceCamera-frame-rate":30,
+    "FaceCamera-1cm-in-pix":480,
+    "RigCamera-frame-rate":20,
+    "RigCamera-1cm-in-pix":33, "TO BE DETERMINED !!":"",
+    "Height-of-Microscope-Camera-Image-in-mm":10000.0, "TO BE DETERMINED !!":"",
+    "rotating-disk":{"radius-position-on-disk-cm":5.5,
+                     "roto-encoder-value-per-rotation": -12563.0},
+    "root_datafolder":"DATA",
+    "subjects_folder":"Adrianna",
+    "experimenter":"Adrianna Nozownik",
+    "lab":"Rebola and Bacci labs",
+    "institution":"Institut du Cerveau et de la Moelle, Paris",
+    "protocols":"all"
+}

{physion-1.0 → physion-1.2}/src/physion/acquisition/configs/Jo-Bacci-2P.json

@@ -3,19 +3,15 @@
     "NIdaq-analog-input-channels":1,
     "NIdaq-digital-input-channels":2,
     "Rig":"Bacci-2P-setup",
-    "Screen":"Dell-2020",
+    "Screen":"Dell-2020",
     "Z-sign-correction-for-rig":1,
     "FaceCamera-frame-rate":30,
     "FaceCamera-1cm-in-pix":480,
     "Height-of-Microscope-Camera-Image-in-mm":10000.0, "TO BE DETERMINED !!":"",
-    "STEP_FOR_CA_IMAGING_TRIGGER":{"channel":0,
-				   "onset": 0.1,
-				   "duration":0.3,
-				   "value":5.0},
     "rotating-disk":{"radius-position-on-disk-cm":5.5,
          		     "roto-encoder-value-per-rotation": -12563.0},
     "root_datafolder":"DATA",
-    "subjects_file":"mice_jo.csv",
+    "subjects_folder":"Jo",
     "experimenter":"Joana Lourenco",
     "lab":"Rebola and Bacci labs",
     "institution":"Institut du Cerveau et de la Moelle, Paris",

{physion-1.0 → physion-1.2}/src/physion/acquisition/configs/Taddy-A1-2P.json

@@ -4,19 +4,15 @@
     "NIdaq-digital-input-channels":2,
     "Screen":"Dell-2020",
     "Rig":"ICM-A1-2P-setup",
-    "Screen":"Dell-2020",
+    "Screen":"Dell-2020",
     "Z-sign-correction-for-rig":-1,
     "FaceCamera-frame-rate":30,
     "FaceCamera-1cm-in-pix":480,
     "Height-of-Microscope-Camera-Image-in-mm":2.7,
-    "STEP_FOR_CA_IMAGING_TRIGGER":{"channel":0,
-				   "onset": 0.1,
-				   "duration":0.3,
-				   "value":5.0},
     "rotating-disk":{"radius-position-on-disk-cm":9.0,
 		     "roto-encoder-value-per-rotation": -25300.0},
     "root_datafolder":"DATA",
-    "subjects_file":"mice_taddy.csv",
+    "subjects_folder":"Taddy",
     "experimenter":"Dhanasak Dhanasobhon",
     "lab":"Rebola and Bacci labs",
     "institution":"Institut du Cerveau et de la Moelle, Paris",

{physion-1.0 → physion-1.2}/src/physion/acquisition/configs/Troubleshooting.json

@@ -5,14 +5,11 @@
     "FaceCamera-frame-rate":30,
     "FaceCamera-1cm-in-pix":480,
     "Screen":"Dell-2020",
-    "STEP_FOR_CA_IMAGING_TRIGGER":{"channel":0,
-				   "onset": 0.1,
-				   "duration":0.3,
-				   "value":5.0},
+    "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},
     "root_datafolder":"DATA",
-    "subjects_file":"mice_yann.json",
+    "subjects_folder":"Yann",
     "experimenter":"Yann Zerlaut",
     "lab":"Rebola and Bacci labs",
     "institution":"Institut du Cerveau et de la Moelle, Paris",

{physion-1.0 → physion-1.2}/src/physion/acquisition/configs/Yann-A1-2P.json

@@ -13,7 +13,7 @@
     "rotating-disk":{"radius-position-on-disk-cm":9.0,
 		     "roto-encoder-value-per-rotation": -25300.0},
     "root_datafolder":"DATA",
-    "subjects_file":"mice_yann.csv",
+    "subjects_folder":"Yann",
     "experimenter":"Yann Zerlaut",
     "lab":"Rebola and Bacci labs",
     "institution":"Institut du Cerveau et de la Moelle, Paris",

{physion-1.0 → physion-1.2}/src/physion/acquisition/configs/Yann-Bacci-2P.json

@@ -1,21 +1,19 @@
 {
-    "NIdaq-acquisition-frequency":200000,
+    "NIdaq-acquisition-frequency":10000,
     "NIdaq-analog-input-channels":1,
     "NIdaq-digital-input-channels":2,
     "Rig":"Bacci-2P-setup",
-    "Screen":"Dell-2020",
+    "Screen":"Dell-2020",
     "Z-sign-correction-for-rig":1,
     "FaceCamera-frame-rate":30,
     "FaceCamera-1cm-in-pix":480,
+    "RigCamera-frame-rate":20,
+    "RigCamera-1cm-in-pix":33, "TO BE DETERMINED !!":"",
     "Height-of-Microscope-Camera-Image-in-mm":10000.0, "TO BE DETERMINED !!":"",
-    "STEP_FOR_CA_IMAGING_TRIGGER":{"channel":0,
-				   "onset": 0.1,
-				   "duration":0.3,
-				   "value":5.0},
     "rotating-disk":{"radius-position-on-disk-cm":5.5,
-         		     "roto-encoder-value-per-rotation": -12563.0},
+                     "roto-encoder-value-per-rotation": -12563.0},
     "root_datafolder":"DATA",
-    "subjects_file":"mice_yann.csv",
+    "subjects_folder":"Yann",
     "experimenter":"Yann Zerlaut",
     "lab":"Rebola and Bacci labs",
     "institution":"Institut du Cerveau et de la Moelle, Paris",

{physion-1.0 → physion-1.2}/src/physion/acquisition/gui.py

@@ -1,7 +1,7 @@
 from PyQt5 import QtWidgets, QtCore
 import sys, time, os, pathlib, json, tempfile
 import numpy as np
-import multiprocessing # different processes (cameras, visual stim, ...) are sent on different threads...
+import multiprocessing # different processes (cameras, visual stim, ...) are sent on different threads...)
 from ctypes import c_char_p
 import pyqtgraph as pg
 import subprocess
@@ -13,6 +13,8 @@ from physion.visual_stim.screens import SCREENS
 from physion.acquisition.settings import load_settings
 from physion.assembling.gui import build_cmd
 
+from physion.acquisition import MODALITIES
+
 def multimodal(self,
                tab_id=0):
 
@@ -23,13 +25,7 @@ def multimodal(self,
 
     self.config = None
     self.subject, self.protocol = None, {}
-    self.MODALITIES = ['Locomotion',
-                       'FaceCamera',
-                       'RigCamera',
-                       'EphysLFP',
-                       'EphysVm',
-                       'CaImaging',
-                       'onlyDemo']
+    self.MODALITIES = MODALITIES
 
     ##########################################
     ######## Multiprocessing quantities  #####
@@ -37,8 +33,6 @@ def multimodal(self,
     # to be used through multiprocessing.Process:
     self.runEvent = multiprocessing.Event() # to turn on/off recordings 
     self.runEvent.clear()
-    self.readyEvent = multiprocessing.Event() # to tell of buffering finished
-    self.readyEvent.clear()
     self.quitEvent = multiprocessing.Event()
     self.quitEvent.clear()
     self.manager = multiprocessing.Manager() # to share a str across processes
@@ -52,7 +46,6 @@ def multimodal(self,
     self.screen, self.stop_flag = None, False
     self.FaceCamera_process = None
     self.RigCamera_process = None
-    self.VisualStim_process = None
     self.RigView_process = None
     self.params_window = None
 
@@ -113,7 +106,7 @@ def multimodal(self,
     #------------------- THEN MAIN PANEL   -------------------
     ip, width = 0, 4
     tab.layout.addWidget(\
-        QtWidgets.QLabel(40*' '+'** Config **', self),
+        QtWidgets.QLabel(40*' '+'** Configuration **', self),
                          ip, self.side_wdgt_length, 
                          1, width)
     ip+=1
@@ -158,6 +151,7 @@ def multimodal(self,
     ip+=1
     # -
     self.protocolBox= QtWidgets.QComboBox(self)
+    # self.protocolBox.activated.connect(self.update_visualStim)
     tab.layout.addWidget(self.protocolBox,\
                          ip, self.side_wdgt_length+1, 
                          1, width)
@@ -195,23 +189,17 @@ def multimodal(self,
 
     # NOW MENU INTERACTION BUTTONS
     ip, width = 1, 5
-    self.initButton = QtWidgets.QPushButton(' * Initialize * ')
-    self.initButton.clicked.connect(self.initialize)
-    tab.layout.addWidget(self.initButton,
-                         ip, 10, 1, width)
-    ip+=2
-    self.runButton = QtWidgets.QPushButton(' * RUN *')
+    self.runButton = QtWidgets.QPushButton(' * START *')
     self.runButton.clicked.connect(self.run)
     tab.layout.addWidget(self.runButton,
                          ip, 10, 1, width)
-    self.runButton.setEnabled(False)
     ip+=1
     self.stopButton = QtWidgets.QPushButton(' * Stop *')
     self.stopButton.clicked.connect(self.stop)
     tab.layout.addWidget(self.stopButton,
                          ip, 10, 1, width)
 
-    for button in [self.initButton, self.runButton, self.stopButton]:
+    for button in [self.runButton, self.stopButton]:
         button.setStyleSheet("font-weight: bold")
 
     ip+=2
@@ -229,14 +217,13 @@ def multimodal(self,
     load_settings(self)
 
     if self.animate_buttons:
-        self.initButton.setEnabled(True)
         self.runButton.setEnabled(False)
         self.stopButton.setEnabled(False)
 
 def build_NWB_for_last():
     # last folder
-    folder = last_datafolder_in_dayfolder(day_folder(FOLDERS['~/DATA']))
-    print(folder)
+    folder = last_datafolder_in_dayfolder(day_folder(FOLDERS[list(FOLDERS.keys())[0]]))
+    print('[ ] build NWB file for recording: ', folder)
     if os.path.isdir(folder):
         cmd, cwd = build_cmd(folder)
         print('\n launching the command \n :  %s \n ' % cmd)

{physion-1.0 → physion-1.2}/src/physion/acquisition/protocols/FFDG-contrast-curve+blank.json

@@ -1,11 +1,13 @@
 {
   "Presentation": "multiprotocol",
   "shuffling" :"full",
-  "shuffling-seed" :34,
+  "shuffling-seed" :34,
+  "movie_refresh_freq":30.0,
+  "units":"cm",
   "Protocol-1": "subprotocols/contrast-curves/ff-drifting-gratings-4orientation-5contrasts-log-spaced-10repeats.json",
   "Protocol-2": "subprotocols/blank/grey-5min.json",
   "Protocol-3": "subprotocols/blank/black-5min.json",
-  "presentation-blank-screen-color": 0,
+  "presentation-blank-screen-color": 0.5,
   "presentation-prestim-period": 2.0,
   "presentation-poststim-period": 2.0,
   "presentation-interstim-period": 4.0,

{physion-1.0 → physion-1.2}/src/physion/acquisition/protocols/Light-Levels-Symmetric-5b-5g-10blank-5g-5b.json

@@ -1,6 +1,8 @@
 {
   "Presentation": "multiprotocol",
-  "shuffling" :"none",
+  "shuffling" :"none",  
+  "movie_refresh_freq":30.0,
+  "units":"cm",
   "Protocol-1": "subprotocols/blank/black-5min.json",
   "Protocol-2": "subprotocols/blank/grey-5min.json",
   "Protocol-3": "subprotocols/blank/black-10min.json",

physion-1.2/src/physion/acquisition/protocols/Millman-et-al-2020.json

@@ -0,0 +1,41 @@
+{
+  "Presentation": "Stimuli-Sequence",
+  "Stimulus": "center-drifting-grating",
+  "Screen": "Dell-2020",
+  "movie_refresh_freq":20,
+  "presentation-duration": 2.0,
+  "presentation-blank-screen-color": 0.5,
+  "presentation-prestim-period": 5.0,
+  "presentation-poststim-period": 5.0,
+  "presentation-interstim-period": 2.0,
+  "units":"cm",
+  "starting-index": 0,
+  "angle-1": 0.0,
+  "angle-2": 315.0,
+  "N-angle": 8,
+  "spatial-freq-1": 0.04,
+  "spatial-freq-2": 0.04,
+  "N-spatial-freq": 0,
+  "speed-1": 1.0,
+  "speed-2": 1.0,
+  "N-speed": 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": 0.05,
+  "contrast-2": 0.8,
+  "N-contrast": 6,
+  "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,
+  "N-repeat": 10
+}

{physion-1.0 → physion-1.2}/src/physion/acquisition/protocols/NDNF-protocol.json

@@ -1,5 +1,8 @@
 {
-  "Presentation": "multiprotocol",
+  "Presentation": "multiprotocol",	
+  "Screen": "Dell-2020",
+  "movie_refresh_freq":30.0,
+  "units":"cm",
   "shuffling" :"full",
   "shuffling-seed" :23,
   "Protocol-1": "subprotocols/NDNF/moving-dots.json",
@@ -7,11 +10,10 @@
   "Protocol-3": "subprotocols/NDNF/static-patch.json",
   "Protocol-4": "subprotocols/NDNF/looming-stim.json",
   "Protocol-5": "subprotocols/NDNF/Natural-Images-4-repeats.json",
-  "Protocol-6": "subprotocols/blank/grey-10min.json",
+  "Protocol-6": "subprotocols/blank/grey-20min.json",
   "Protocol-7": "subprotocols/NDNF/drifting-gratings.json",
   "presentation-blank-screen-color": 0.5,
   "presentation-prestim-period": 6,
   "presentation-poststim-period": 6,
-  "presentation-interstim-period": 4,
-  "Screen": "Dell-2020"
+  "presentation-interstim-period": 4
 }

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-1.0 → physion-1.2}/src/physion/acquisition/protocols/drifting-gratings.json

@@ -2,21 +2,22 @@
   "Presentation": "Stimuli-Sequence",
   "Stimulus": "center-drifting-grating",
   "Screen": "Dell-2020",
-  "movie_refresh_freq":20,
+  "movie_refresh_freq":30.0,
+  "units":"cm",
   "presentation-duration": 3.0,
-  "presentation-blank-screen-color": 0,
+  "presentation-blank-screen-color": 0.5,
   "presentation-prestim-period": 6.0,
   "presentation-poststim-period": 6.0,
   "presentation-interstim-period": 6.0,
-  "starting-index": 0,
+  "N-repeat": 10,
   "angle-1": 0.0,
   "angle-2": 270.0,
   "N-angle": 4,
-  "spatial-freq-1": 0.1,
-  "spatial-freq-2": 0.1,
+  "spatial-freq-1": 0.05,
+  "spatial-freq-2": 0.05,
   "N-spatial-freq": 0,
-  "speed-1": 2.0,
-  "speed-2": 2.0,
+  "speed-1": 1.0,
+  "speed-2": 1.0,
   "N-speed": 0,
   "radius-1": 200,
   "radius-2": 200,
@@ -27,11 +28,13 @@
   "y-center-1": 0.0,
   "y-center-2": 0.0,
   "N-y-center": 0,
-  "contrast-1": 1.0,
+  "contrast-1": 0.2,
   "contrast-2": 1.0,
-  "N-contrast": 0,
+  "N-contrast": 3,
   "bg-color-1": 0.5,
   "bg-color-2": 0.5,
   "N-bg-color": 0,
-  "N-repeat": 10
+  "phase-1": 90.0,
+  "phase-2": 90.0,
+  "N-phase": 0
 }

physion-1.2/src/physion/acquisition/protocols/ff-gratings-2orientations-8contrasts-15repeats.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": 4,
+  "presentation-poststim-period": 4,
+  "presentation-interstim-period": 4,
+  "presentation-blank-screen-color": 0.5,
+  "N-repeat": 15,
+  "angle-1": 0,
+  "angle-2": 90,
+  "N-angle": 2,
+  "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": 0.05,
+  "contrast-2": 1.0,
+  "N-contrast": 8,
+  "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-1.2/src/physion/acquisition/protocols/ff-gratings-8orientation-2contrasts-15repeats.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": 4,
+  "presentation-poststim-period": 4,
+  "presentation-interstim-period": 4,
+  "presentation-blank-screen-color": 0.5,
+  "N-repeat": 15,
+  "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": 0.5,
+  "contrast-2": 1.0,
+  "N-contrast": 2,
+  "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
+}