Tests

.gitignore

@@ -1,3 +1,24 @@
+# Data needed by notebooks, should be retrieved by running download_data.sh
+notebooks/eventseg/Sherlock_AG_movie.npy
+notebooks/eventseg/Sherlock_AG_recall.npy
+notebooks/fmrisim/Corr_MVPA_Data_dataspace/
+notebooks/fmrisim/Corr_MVPA_archive.tar.gz
+notebooks/isc/brainiak-aperture-isc-data/
+notebooks/srm/brainiak-aperture-srm-data/
+notebooks/fmrisim/Corr_MVPA/
+notebooks/iem/AL61_Bilat-V1_attnContrast.mat
+notebooks/iem/RademakerEtAl2019_WM_S05_avgTime.npz
+notebooks/isc/brainiak-aperture-isc-data.tgz
+notebooks/srm/brainiak-aperture-srm-data.tgz
+notebooks/htfa/data
+notebooks/real-time/sample-config.toml
+
+# Files generated when running fmrisim notebook
+notebooks/fmrisim/Condition_A.txt
+notebooks/fmrisim/Condition_B.txt
+notebooks/fmrisim/epoch_file.npy
+
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -133,4 +154,4 @@ dmypy.json
 .DS_Store
 
 # htfa temp files
-notebooks/htfa/*_frames/*.jpg
+notebooks/htfa/*_frames/*.jpg

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "notebooks/real-time/rt-cloud"]
+	path = notebooks/real-time/rt-cloud
+	url = https://github.com/brainiak/rt-cloud.git

download_data.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+find notebooks -name 'download_data.sh' -execdir bash download_data.sh \;

notebooks/brsa/requirements.txt

@@ -0,0 +1,4 @@
+scipy
+numpy
+brainiak
+matplotlib

notebooks/eventseg/download_data.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+wget -nc https://ndownloader.figshare.com/files/22927253 -O Sherlock_AG_movie.npy
+wget -nc https://ndownloader.figshare.com/files/22927256 -O Sherlock_AG_recall.npy

notebooks/eventseg/requirements.txt

@@ -0,0 +1,4 @@
+numpy
+matplotlib
+brainiak
+scipy

notebooks/fcma/requirements.txt

@@ -0,0 +1,11 @@
+nxviz<=0.6.3
+pandas
+brainiak
+mpi4py
+nilearn
+matplotlib
+seaborn
+networkx
+nibabel
+numpy
+scikit_learn

notebooks/fmrisim/download_data.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+# Download the archive containing the example data if we don't have it already
+wget -nc https://dataspace.princeton.edu/bitstream/88435/dsp01dn39x4181/2/Corr_MVPA_archive.tar.gz
+
+# If the file doesn't exist, we need to extract it.
+test ! -e Corr_MVPA && tar xzkvf Corr_MVPA_archive.tar.gz Corr_MVPA_Data_dataspace/Participant_01_rest_run01.nii && mv Corr_MVPA_Data_dataspace Corr_MVPA
+

notebooks/fmrisim/fmrisim_multivariate_example.ipynb

@@ -111,7 +111,7 @@
    "source": [
     "*1.2 Load participant data*<a id=\"load_ppt\"></a>\n",
     "\n",
-    "Any 4 dimensional fMRI data that is readible by nibabel can be used as input to this pipeline. For this example, data is taken from the open access repository DataSpace: http://arks.princeton.edu/ark:/88435/dsp01dn39x4181. This file is unzipped and placed in the home directory with the name Corr_MVPA "
+    "Any 4 dimensional fMRI data that is readible by nibabel can be used as input to this pipeline. For this example, data is taken from the open access repository DataSpace: http://arks.princeton.edu/ark:/88435/dsp01dn39x4181. This file is unzipped and placed same directory as this notebook with the name Corr_MVPA "
    ]
   },
   {
@@ -122,8 +122,7 @@
    },
    "outputs": [],
    "source": [
-    "home = str(Path.home())\n",
-    "nii = nibabel.load(home + '/Corr_MVPA/Participant_01_rest_run01.nii')\n",
+    "nii = nibabel.load('Corr_MVPA/Participant_01_rest_run01.nii')\n",
     "volume = nii.get_data()"
    ]
   },
@@ -5453,18 +5452,18 @@
    "outputs": [],
    "source": [
     "fmrisim.export_epoch_file(stimfunction=[np.hstack((stimfunc_A, stimfunc_B))],\n",
-    "                          filename=home + '/epoch_file.npy',\n",
+    "                          filename='epoch_file.npy',\n",
     "                          tr_duration=tr,\n",
     "                          temporal_resolution=temporal_res,\n",
     "                          )\n",
     "\n",
     "fmrisim.export_3_column(stimfunction=stimfunc_A,\n",
-    "                        filename=home + '/Condition_A.txt',\n",
+    "                        filename='Condition_A.txt',\n",
     "                        temporal_resolution=temporal_res,\n",
     "                        )\n",
     "\n",
     "fmrisim.export_3_column(stimfunction=stimfunc_B,\n",
-    "                        filename=home + '/Condition_B.txt',\n",
+    "                        filename='Condition_B.txt',\n",
     "                        temporal_resolution=temporal_res,\n",
     "                        )"
    ]

notebooks/fmrisim/requirements.txt

@@ -0,0 +1,6 @@
+matplotlib
+nibabel
+scipy
+numpy
+brainiak
+scikit_learn

notebooks/htfa/download_data.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+if [ -d "data/" ]; then
+    echo "Skipping download of data for HTFA notebook, already present"
+else
+    mkdir data
+    wget --save-cookies cookies.txt --keep-session-cookies --no-check-certificate -q \
+        "https://docs.google.com/uc?export=download&id=1IBA39ZZjeGS1u_DvZdiw1AZZQMS3K5q0" -O- \
+        | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\1\n/p' > confirm
+    wget --load-cookies cookies.txt --no-check-certificate -q \
+        "https://docs.google.com/uc?export=download&confirm="$(cat confirm)"&id=1IBA39ZZjeGS1u_DvZdiw1AZZQMS3K5q0" -O data/pieman.zip
+    rm cookies.txt confirm
+    unzip data/pieman.zip -d data/
+    rm data/pieman.zip
+fi
+

notebooks/htfa/requirements.txt

@@ -0,0 +1,12 @@
+holoviews
+numpy
+pandas
+brainiak
+nilearn
+timecorr
+matplotlib
+mpi4py
+nibabel
+seaborn
+nltools
+ipython

notebooks/iem/download_data.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+wget -nc https://zenodo.org/record/4950267/files/RademakerEtAl2019_WM_S05_avgTime.npz
+wget -nc https://zenodo.org/record/4950267/files/AL61_Bilat-V1_attnContrast.mat

notebooks/iem/requirements.txt

@@ -0,0 +1,5 @@
+scipy
+brainiak
+numpy
+matplotlib
+scikit_learn

notebooks/isc/ISC.ipynb

@@ -40,7 +40,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -75,25 +75,15 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "--2020-12-07 01:33:28--  https://zenodo.org/record/4300904/files/brainiak-aperture-isc-data.tgz\n",
-      "Resolving zenodo.org (zenodo.org)... 137.138.76.77\n",
-      "Connecting to zenodo.org (zenodo.org)|137.138.76.77|:443... connected.\n",
-      "HTTP request sent, awaiting response... 200 OK\n",
-      "Length: 3146248838 (2.9G) [application/octet-stream]\n",
-      "Saving to: ‘brainiak-aperture-isc-data.tgz’\n",
-      "\n",
-      "brainiak-aperture-i 100%[===================>]   2.93G  6.53MB/s    in 4m 32s  \n",
-      "\n",
-      "2020-12-07 01:38:02 (11.0 MB/s) - ‘brainiak-aperture-isc-data.tgz’ saved [3146248838/3146248838]\n",
+      "File ‘brainiak-aperture-isc-data.tgz’ already there; not retrieving.\n",
       "\n"
      ]
     }
    ],
    "source": [
     "# Download and extract example data from Zenodo\n",
-    "!wget https://zenodo.org/record/4300904/files/brainiak-aperture-isc-data.tgz\n",
-    "!tar -xzf brainiak-aperture-isc-data.tgz\n",
-    "!rm brainiak-aperture-isc-data.tgz"
+    "!wget -nc https://zenodo.org/record/4300904/files/brainiak-aperture-isc-data.tgz\n",
+    "!tar --skip-old-files -xzf brainiak-aperture-isc-data.tgz\n"
    ]
   },
   {
@@ -637,9 +627,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "brainiak_pr_venv_ORLfW",
    "language": "python",
-   "name": "python3"
+   "name": "brainiak_pr_venv_orlfw"
   },
   "language_info": {
    "codemirror_mode": {
@@ -651,7 +641,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.7"
+   "version": "3.8.11"
   }
  },
  "nbformat": 4,

notebooks/isc/download_data.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+# Download the data, the python notebook handles extraction and
+wget -nc https://zenodo.org/record/4300904/files/brainiak-aperture-isc-data.tgz

notebooks/isc/requirements.txt

@@ -0,0 +1,7 @@
+matplotlib
+scipy
+seaborn
+brainiak
+nibabel
+numpy
+nilearn

notebooks/matnormal/requirements.txt

@@ -0,0 +1,7 @@
+tensorflow
+numpy
+matplotlib
+brainiak
+seaborn
+scipy
+scikit_learn

notebooks/real-time/requirements.txt

@@ -0,0 +1,31 @@
+awscli
+bcrypt
+bids
+brainiak
+dicom
+indexed_gzip
+inflect
+inotify
+ipython
+jupyter
+matplotlib
+mypy
+nibabel
+nilearn
+nodejs
+numpy
+pandas
+pybids
+pydicom
+pyOpenSSL
+python_bcrypt
+python_dateutil
+requests
+rpyc
+scikit_learn
+scipy
+toml
+tornado
+watchdog
+websocket_client
+wsaccel

notebooks/real-time/rtcloud_notebook.ipynb

@@ -54,6 +54,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "# If rt-cloud repo is present in local directory and RTCLOUD_PATH is not already set, \n",
+    "# then set RTCLOUD_PATH to the local repo.\n",
+    "import os\n",
+    "if 'RTCLOUD_PATH' not in os.environ and os.path.exists('rt-cloud'):\n",
+    "    os.environ['RTCLOUD_PATH'] = os.path.abspath('rt-cloud')\n",
+    "\n",
     "!echo $RTCLOUD_PATH"
    ]
   },
@@ -73,7 +79,6 @@
     "import warnings; warnings.simplefilter('ignore')\n",
     "\n",
     "#---- Import the necessary python modules\n",
-    "import os\n",
     "import sys\n",
     "import threading\n",
     "import argparse\n",
@@ -279,9 +284,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "%%html\n",
@@ -299,7 +302,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Instead of running the classification script from the web browser (as above), it can be run from the command line. The command below will run the sample.py script (of the real-time aperture notebook) as if running on the command line."
+    "Instead of running the classification script from the web browser (as above), it can be run directly by running the scripts main function. "
    ]
   },
   {
@@ -308,8 +311,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Run the classification script from the command line instead of from the browser interface\n",
-    "!python -u $scriptToRun -c $configFile"
+    "# Run the classification script directly by importing the scripts main function.\n",
+    "from sample import main\n",
+    "main(['-c', configFile])"
    ]
   },
   {
@@ -328,7 +332,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -342,7 +346,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.11"
+   "version": "3.8.3"
   }
  },
  "nbformat": 4,

notebooks/srm/SRM.ipynb

@@ -94,9 +94,8 @@
    ],
    "source": [
     "# Download and extract example data from Zenodo\n",
-    "!wget https://zenodo.org/record/4300825/files/brainiak-aperture-srm-data.tgz\n",
-    "!tar -xzf brainiak-aperture-srm-data.tgz\n",
-    "!rm brainiak-aperture-srm-data.tgz"
+    "!wget -nc https://zenodo.org/record/4300825/files/brainiak-aperture-srm-data.tgz\n",
+    "!tar --skip-old-files -xzf brainiak-aperture-srm-data.tgz\n"
    ]
   },
   {
@@ -556,7 +555,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.12"
+   "version": "3.8.3"
   }
  },
  "nbformat": 4,

notebooks/srm/download_data.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+wget -nc https://zenodo.org/record/4300825/files/brainiak-aperture-srm-data.tgz

notebooks/srm/requirements.txt

@@ -0,0 +1,7 @@
+brainiak
+matplotlib
+nibabel
+nilearn
+seaborn
+numpy
+scipy