Update curation (#44)

brainglobe · Feb 12, 2020 · 9b0d5a8 · 9b0d5a8
1 parent a627661
commit 9b0d5a8
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Showing 8 changed files with 18 additions and 11 deletions.
diff --git a/cellfinder/__init__.py b/cellfinder/__init__.py
@@ -1,3 +1,3 @@
-__version__ = "0.3.6"
+__version__ = "0.3.7"
 __author__ = "Adam Tyson, Christian Niedworok, Charly Rousseau"
 __license__ = "GPL-3.0"
diff --git a/cellfinder/train/curation.py b/cellfinder/train/curation.py
@@ -88,9 +88,9 @@ def main():
             f"directory to: {output_directory}"
         )
     else:
-        output_directory = args.output
+        output_directory = Path(args.output)
 
-    ensure_directory_exists(output_directory)
+    ensure_directory_exists(str(output_directory))
     output_filename = output_directory / OUTPUT_NAME
 
     img_paths = get_sorted_file_paths(
@@ -232,9 +232,11 @@ def run_extraction(
     save_empty_cubes,
 ):
     planes_paths = {}
-    planes_paths[0] = get_sorted_file_paths(signal_paths, file_extension="tif")
+    planes_paths[0] = get_sorted_file_paths(
+        signal_paths, file_extension=".tif"
+    )
     planes_paths[1] = get_sorted_file_paths(
-        background_paths, file_extension="tif"
+        background_paths, file_extension=".tif"
     )
 
     all_candidates = get_cells(str(output_filename))

diff --git a/cellfinder/viewer/two_dimensional.py b/cellfinder/viewer/two_dimensional.py
@@ -45,7 +45,7 @@ def get_cell_arrays(cells_file):
 
 
 def estimate_image_max(image_paths, multiplier=2):
-    centre_plane = int(len(image_paths)/2)
+    centre_plane = int(len(image_paths) / 2)
     max_value = imread(image_paths[centre_plane]).max()
     return int(multiplier * max_value)
 

diff --git a/docs/_static/basic.css b/docs/_static/basic.css
@@ -672,6 +672,10 @@ div.code-block-caption + div > div.highlight > pre {
     margin-top: 0;
 }
 
+div.doctest > div.highlight span.gp {  /* gp: Generic.Prompt */
+    user-select: none;
+}
+
 div.code-block-caption span.caption-number {
     padding: 0.1em 0.3em;
     font-style: italic;

diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
@@ -3,6 +3,7 @@ var DOCUMENTATION_OPTIONS = {
     VERSION: '',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
+    BUILDER: 'html',
     FILE_SUFFIX: '.html',
     HAS_SOURCE: true,
     SOURCELINK_SUFFIX: '.txt',

diff --git a/docs/_static/searchtools.js b/docs/_static/searchtools.js
@@ -245,7 +245,7 @@ var Search = {
       if (results.length) {
         var item = results.pop();
         var listItem = $('<li style="display:none"></li>');
-        if (DOCUMENTATION_OPTIONS.FILE_SUFFIX === '') {
+        if (DOCUMENTATION_OPTIONS.BUILDER === 'dirhtml') {
           // dirhtml builder
           var dirname = item[0] + '/';
           if (dirname.match(/\/index\/$/)) {
@@ -424,15 +424,15 @@ var Search = {
         for (j = 0; j < _files.length; j++) {
           file = _files[j];
           if (!(file in scoreMap))
-            scoreMap[file] = {}
+            scoreMap[file] = {};
           scoreMap[file][word] = o.score;
         }
       });
 
       // create the mapping
       for (j = 0; j < files.length; j++) {
         file = files[j];
-        if (file in fileMap)
+        if (file in fileMap && fileMap[file].indexOf(word) === -1)
           fileMap[file].push(word);
         else
           fileMap[file] = [word];

diff --git a/docs/searchindex.js b/docs/searchindex.js
diff --git a/setup.py b/setup.py
@@ -88,7 +88,7 @@
 
 setup(
     name="cellfinder",
-    version="0.3.6",
+    version="0.3.7",
     description="Cell detection for whole-brain microscopy",
     install_requires=requirements,
     extras_require={