Merge branch 'master' of github.com:karanphil/scilpy into set_frf_msmt

.github/workflows/test.yml

@@ -4,7 +4,7 @@ on:
   push:
     branches:
       - master
-  pull_request_target:
+  pull_request:
     branches:
       - master
 
@@ -20,7 +20,7 @@ jobs:
   test:
     runs-on: scilus-runners
     steps:
-      - name: Checkout repository
+      - name: Checkout repository for merge
         uses: actions/[email protected]
 
       - name: Fetch python version from repository

scilpy/io/fetcher.py

@@ -1,15 +1,17 @@
 # -*- coding: utf-8 -*-
+
 import logging
 import hashlib
 import os
 import pathlib
 import requests
 import zipfile
 
-GOOGLE_URL = "https://drive.usercontent.google.com/download?"
+
+DVC_URL = "https://scil.usherbrooke.ca/scil_test_data/dvc-store/files/md5"
 
 
-def download_file_from_google_drive(id, destination):
+def download_file_from_google_drive(url, destination):
     """
     Download large file from Google Drive.
     Parameters
@@ -19,13 +21,6 @@ def download_file_from_google_drive(id, destination):
     destination: str
         path to destination file with its name and extension
     """
-    def get_confirm_token(response):
-        for key, value in response.cookies.items():
-            if key.startswith('download_warning'):
-                return value
-
-        return None
-
     def save_response_content(response, destination):
         CHUNK_SIZE = 32768
 
@@ -34,13 +29,7 @@ def save_response_content(response, destination):
                 f.write(chunk)
 
     session = requests.Session()
-    params = {'id': id, 'confirm': True}
-    response = session.get(GOOGLE_URL, params=params, stream=True)
-    token = get_confirm_token(response)
-
-    if token:
-        params['confirm'] = token
-        response = session.get(GOOGLE_URL, params=params, stream=True)
+    response = session.get(url, stream=True)
 
     save_response_content(response, destination)
 
@@ -56,66 +45,28 @@ def get_home():
 
 def get_testing_files_dict():
     """ Get dictionary linking zip file to their GDrive ID & MD5SUM """
-    return {'bids_json.zip':
-            ['1bMl5YtEufoKh-gjen940QTO5BpT5Y9TF',
-             '521eed4911c456cc10cc3cb1f6a5dc83'],
-            'plot.zip':
-            ['1Ab-oVWI1Fu7fHTEz1H3-s1TfR_oW-GOE',
-             'cca8f1e19da357f44365a7e27b9029ca'],
-            'ihMT.zip':
-            ['1V0xzvmVrVlL9dRKhc5-7xWESkmof1zyS',
-             '5d28430ac46b4fc04b6d77f9efaefb5c'],
-            'MT.zip':
-            ['1C2LEUkGaLFdsmym3kBrAtfPjPtv5mJuZ',
-             '13532c593efdf09350667df14ea4e93a'],
-            'atlas.zip':
-            ['1waYx4ED3qwzyJqrICjjgGXXBW2v4ZCYJ',
-             'eb37427054cef5d50ac3d429ff53de47'],
-            'bst.zip':
-            ['1YprJRnyXk7VRHUkb-bJLs69C1v3tPd1S',
-             'c0551a28dcefcd7cb53f572b1794b3e8'],
-            'bundles.zip':
-            ['1VaGWwhVhnfsZBCCYu12dta9qi0SgZFP7',
-             '5fbf5c8eaabff2648ad509e06b003e67'],
-            'commit_amico.zip':
-            ['1vyMtQd1u2h2pza9M0bncDWLc34_4MRPK',
-             'b40800ab4290e4f58c375140fe59b44f'],
-            'connectivity.zip':
-            ['1lZqiOKmwTluPIRqblthOnBc4KI2kfKUC',
-             '6d13bd076225fa2f786f416fa754623a'],
-            'filtering.zip':
-            ['1yzHSL4tBtmm_aeI1i0qJhrA9z040k0im',
-             'dbe796fb75c3e1e5559fad3308982769'],
-            'others.zip':
-            ['12BAszPjE1A9L2RbQJIFpkPzqUJfPdYO6',
-             '981dccd8b23aad43aa014f4fdd907e70'],
-            'processing.zip':
-            ['1caaKoAChyPs5c4WemQWUsR-efD_q2z_b',
-             'a2f982b8d84833f5ccfe709b725307d2'],
-            'surface_vtk_fib.zip':
-            ['1c9KMNFeSkyYDgu3SH_aMf0kduIlpt7cN',
-             'bf131869a6722778a234869bf585520a'],
-            'tracking.zip':
-            ['1QSekZYDoMvv-An6FRMSt_s_qPeB3BHfw',
-             '6d88910403fb4d9b79604f11100d8915'],
-            'tractograms.zip':
-            ['1f98s0TP-862KtB_xsSmRNrmi2nrqRaNU',
-             '911bc59dfdcee3656564f212ae8ed3a1'],
-            'tractometry.zip':
-            ['130mxBo4IJWPnDFyOELSYDif1puRLGHMX',
-             '3e27625a1e7f2484b7fa5028c95324cc'],
-            'stats.zip':
-            ['1vsM7xuU0jF5fL5PIgN6stAH7oO683tw0',
-             '03aed629dea754bbc2041e7ab5f94112'],
-            'anatomical_filtering.zip':
-            ['1Li8DdySnMnO9Gich4pilhXisjkjz1-Dy',
-             '6f0eff5154ff0973a3dc26db00e383ea'],
-            'btensor_testdata.zip':
-            ['1AMsKlbOZyPnT9TAbxcFzHS1b29aJWKDg',
-             '7c68524fca01268203dc8bfee340f037'],
-            'fodf_filtering.zip':
-            ['1iyoX2ltLOoLer-v-49LHOzopHCFZ_Tv6',
-             'e79c4291af584fdb25814aa7b403a6ce']}
+    return {
+        "commit_amico.zip": "c190e6b9d22350b51e222c60febe13b4",
+        "bundles.zip": "54b6e2bf2dda579886efe4e2a8989486",
+        "stats.zip": "2aeac4da5ab054b3a460fc5fdc5e4243",
+        "bst.zip": "eed227fd246255e7417f92d49eb1066a",
+        "filtering.zip": "19116ff4244d057c8214ee3fe8e05f71",
+        "ihMT.zip": "08fcf44848ba2649aad5a5a470b3cb06",
+        "tractometry.zip": "890bfa70e44b15c0d044085de54e00c6",
+        "bids_json.zip": "97fd9a414849567fbfdfdb0ef400488b",
+        "MT.zip": "1f4345485248683b3652c97f2630950e",
+        "btensor_testdata.zip": "7ada72201a767292d56634e0a7bbd9ad",
+        "tracking.zip": "4793a470812318ce15f1624e24750e4d",
+        "atlas.zip": "dc34e073fc582476504b3caf127e53ef",
+        "anatomical_filtering.zip": "5282020575bd485e15d3251257b97e01",
+        "connectivity.zip": "fe8c47f444d33067f292508d7050acc4",
+        "plot.zip": "a1dc54cad7e1d17e55228c2518a1b34e",
+        "others.zip": "82248b4888a63b0aeffc8070cc206995",
+        "fodf_filtering.zip": "5985c0644321ecf81fd694fb91e2c898",
+        "processing.zip": "eece5cdbf437b8e4b5cb89c797872e28",
+        "surface_vtk_fib.zip": "241f3afd6344c967d7176b43e4a99a41",
+        "tractograms.zip": "5497d0bf3ccc35f8f4f117829d790267"
+    }
 
 
 def fetch_data(files_dict, keys=None):
@@ -134,23 +85,23 @@ def fetch_data(files_dict, keys=None):
     elif isinstance(keys, str):
         keys = [keys]
     for f in keys:
-        url_id, md5 = files_dict[f]
+        url_md5 = files_dict[f]
         full_path = os.path.join(scilpy_home, f)
         full_path_no_ext, ext = os.path.splitext(full_path)
 
-        CURR_URL = GOOGLE_URL + 'id=' + url_id
+        CURR_URL = DVC_URL + "/" + url_md5[:2] + "/" + url_md5[2:]
         if not os.path.isdir(full_path_no_ext):
             if ext == '.zip' and not os.path.isdir(full_path_no_ext):
                 logging.warning('Downloading and extracting {} from url {} to '
                                 '{}'.format(f, CURR_URL, scilpy_home))
 
                 # Robust method to Virus/Size check from GDrive
-                download_file_from_google_drive(url_id, full_path)
+                download_file_from_google_drive(CURR_URL, full_path)
 
                 with open(full_path, 'rb') as file_to_check:
                     data = file_to_check.read()
                     md5_returned = hashlib.md5(data).hexdigest()
-                if md5_returned != md5:
+                if md5_returned != url_md5:
                     try:
                         zipfile.ZipFile(full_path)
                     except zipfile.BadZipFile:

scripts/scil_visualize_connectivity.py

@@ -238,11 +238,13 @@ def main():
             logging.warning('Legend is not the same size as the data.'
                             'Make sure you are using the same reordering '
                             'json.')
+
         plt.xticks(x_ticks, x_legend,
-                   rotation=args.axis_text_angle[0],
+                   rotation=int(args.axis_text_angle[0]),
+                   ha='right',
                    fontsize=args.axis_text_size[0])
         plt.yticks(y_ticks, y_legend,
-                   rotation=args.axis_text_angle[1],
+                   rotation=int(args.axis_text_angle[1]),
                    fontsize=args.axis_text_size[1])
 
     if args.show_only: