Code quality: fix PEP8 violations

synapsesuggestor/admin.py

@@ -18,9 +18,11 @@
 
 admin.site.register(SynapseDetectionTile)
 
+
 class SynapseSliceAdmin(admin.ModelAdmin):
     pass
 
+
 admin.site.register(SynapseSlice, SynapseSliceAdmin)
 
 admin.site.register(SynapseObject)

synapsesuggestor/control/analysis.py

@@ -3,7 +3,6 @@
 Methods called by the frontend analysis widget
 """
 from __future__ import division
-import numpy as np
 
 from django.db import connection
 from django.http import JsonResponse
@@ -77,25 +76,27 @@ def get_skeleton_synapses(request, project_id=None):
     if ssw_id is None:
         pssw = get_most_recent_project_SS_workflow(project_id)
     else:
-        pssw = ProjectSynapseSuggestionWorkflow.objects.get(synapse_suggestion_workflow_id=ssw_id, project_id=project_id)
+        pssw = ProjectSynapseSuggestionWorkflow.objects.get(
+            synapse_suggestion_workflow_id=ssw_id, project_id=project_id
+        )
 
     cursor = connection.cursor()
 
     # todo: why is this casting necessary? unit tests produced strings
     cursor.execute('''
-        SELECT 
+        SELECT
             ss_so_synapse_object_id, array_agg(tn_id), tn_skeleton_id,
-            cast(round(avg(that_ss_xs_centroid)) as int), cast(round(avg(that_ss_ys_centroid)) as int), 
+            cast(round(avg(that_ss_xs_centroid)) as int), cast(round(avg(that_ss_ys_centroid)) as int),
             cast(round(avg(tile_z_tile_idx)) as int), array_agg(tile_z_tile_idx),
             sum(that_ss_size_px), sum(ss_tn_contact_px), avg(that_ss_uncertainty)
         FROM (
-            SELECT DISTINCT ON (that_ss.id) 
+            SELECT DISTINCT ON (that_ss.id)
               ss_so.synapse_object_id, tn.id, tn.skeleton_id,
               that_ss.xs_centroid, that_ss.ys_centroid, tile.z_tile_idx,
               that_ss.size_px, ss_tn.contact_px, that_ss.uncertainty
             FROM treenode tn
               INNER JOIN synapse_slice_treenode ss_tn
-                ON tn.id = ss_tn.treenode_id 
+                ON tn.id = ss_tn.treenode_id
               INNER JOIN synapse_slice this_ss
                 ON ss_tn.synapse_slice_id = this_ss.id
               INNER JOIN synapse_slice_synapse_object ss_so
@@ -223,9 +224,9 @@ def _get_intersecting_connectors_edge(cursor=None, **kwargs):
           SELECT subq.syn_id, subq.c_id, subq.c_x, subq.c_y, subq.c_z, subq.c_conf, subq.c_user,
             array_agg(tn.skeleton_id), array_agg(tn.id), subq.min_dist
           FROM (
-            SELECT 
-              ss_so.synapse_object_id, 
-              c.id, c.location_x, c.location_y, c.location_z, c.confidence, c.user_id, 
+            SELECT
+              ss_so.synapse_object_id,
+              c.id, c.location_x, c.location_y, c.location_z, c.confidence, c.user_id,
               min(ST_Distance(tce.edge, ss_trans.geom_2d))
             FROM synapse_slice_synapse_object ss_so
             INNER JOIN unnest(%(obj_ids)s::BIGINT[]) AS syns (id)
@@ -271,8 +272,8 @@ def _get_intersecting_connectors_node(cursor=None, **kwargs):
         array_agg(tn.skeleton_id), array_agg(tn.id), subq.min_dist
       FROM (
         SELECT
-          ss_so.synapse_object_id, 
-          c.id, c.location_x, c.location_y, c.location_z, c.confidence, c.user_id, 
+          ss_so.synapse_object_id,
+          c.id, c.location_x, c.location_y, c.location_z, c.confidence, c.user_id,
           min(ST_Distance(ST_MakePoint(c.location_x, c.location_y), ss_trans.geom_2d))
         FROM synapse_slice_synapse_object ss_so
         INNER JOIN unnest(%(obj_ids)s::BIGINT[]) AS syns (id)
@@ -288,7 +289,8 @@ def _get_intersecting_connectors_node(cursor=None, **kwargs):
           ON ss_trans.synapse_detection_tile_id = tile.id
         INNER JOIN connector c
           ON (tile.z_tile_idx + %(offset_zs)s) * %(resolution_z)s = c.location_z
-          AND ST_DWithin(ST_MakePoint(c.location_x, c.location_y), ss_trans.geom_2d, %(tolerance)s)  -- better way to handle geom?
+          -- better way to handle geom?
+          AND ST_DWithin(ST_MakePoint(c.location_x, c.location_y), ss_trans.geom_2d, %(tolerance)s)
           AND c.project_id = %(project_id)s
         GROUP BY ss_so.synapse_object_id, c.id
       ) AS subq (syn_id, c_id, c_x, c_y, c_z, c_conf, c_user, min_dist)
@@ -346,7 +348,7 @@ def get_synapse_extents(request, project_id=None):
             min(ST_YMin(ss.geom_2d)) - %(xy_pad)s, max(ST_YMax(ss.geom_2d)) + %(xy_pad)s,
             min(tile.z_tile_idx) - %(z_pad)s, max(tile.z_tile_idx) + %(z_pad)s
           FROM synapse_slice_synapse_object ss_so
-          INNER JOIN synapse_slice ss 
+          INNER JOIN synapse_slice ss
             ON ss_so.synapse_slice_id = ss.id
           INNER JOIN synapse_detection_tile tile
             ON ss.synapse_detection_tile_id = tile.id
@@ -388,7 +390,7 @@ def get_partners(request, project_id=None):
     cursor = connection.cursor()
 
     cursor.execute('''
-        SELECT 
+        SELECT
             ss_so.synapse_object_id, array_agg(tn.id), tn.skeleton_id, sum(ss_tn.contact_px)
           FROM synapse_slice_synapse_object ss_so
           INNER JOIN unnest(%(syns)s::bigint[]) AS syns(id)

synapsesuggestor/control/common.py

@@ -36,7 +36,8 @@ def list_into_query(query, arg_lst, fmt='%s'):
     Args:
       query(str): A string with a single {} in it
       arg_lst(list): List of arguments to supply to SQL
-      fmt(str, optional): Placeholder to use for each element (e.g. use this to wrap stuff in brackets), or to account for tuples (Default value = '%s')
+      fmt(str, optional): Placeholder to use for each element (e.g. use this to wrap stuff in brackets), or to account
+        for tuples (Default value = '%s')
 
     Returns:
       (str, tuple): The two arguments to pass to cursor.execute
@@ -74,8 +75,8 @@ def list_into_query_multi(query, fmt=None, **kwargs):
     --------
     >>> query = "INSERT INTO table_name1 (a, b) VALUES ({first}); INSERT INTO table_name2 (a, b) VALUES ({second});"
     >>> list_into_query_multi(query, fmt={'second': '(%s, %s)'}, first=[1, 2, 3], second=[[1,2], [3,4]])
-    >>> ('INSERT INTO table_name1 (a, b) VALUES (%s, %s, %s); INSERT INTO table_name2 (a, b) VALUES ((%s, %s), (%s, %s));',
-    >>>     [1, 2, 3, 1, 2, 3, 4])
+    ('INSERT INTO table_name1 (a, b) VALUES (%s, %s, %s); INSERT INTO table_name2 (a, b) VALUES ((%s, %s), (%s, %s));',
+         [1, 2, 3, 1, 2, 3, 4])
     """
     if fmt is None:
         fmt = dict()
@@ -112,9 +113,9 @@ def get_translation_resolution(project_id, ssw_id, cursor=None):
         cursor = connection.cursor()
 
     cursor.execute('''
-        SELECT 
-          (ps.translation).x, (ps.translation).y, (ps.translation).z, 
-          (stack.resolution).x, (stack.resolution).y, (stack.resolution).z  
+        SELECT
+          (ps.translation).x, (ps.translation).y, (ps.translation).z,
+          (stack.resolution).x, (stack.resolution).y, (stack.resolution).z
         FROM synapse_suggestion_workflow ssw
           INNER JOIN synapse_detection_tiling tiling
             ON ssw.synapse_detection_tiling_id = tiling.id

synapsesuggestor/control/synapse_detection.py

@@ -11,7 +11,7 @@
 from django.http import JsonResponse
 from rest_framework.decorators import api_view
 
-from catmaid.control.authentication import requires_user_role
+# from catmaid.control.authentication import requires_user_role
 from catmaid.control.common import get_request_list
 from synapsesuggestor.control.common import list_into_query
 from synapsesuggestor.models import SynapseDetectionTile, SynapseObject

synapsesuggestor/control/treenode_association.py

@@ -9,15 +9,17 @@
 from django.http import JsonResponse
 from rest_framework.decorators import api_view
 
-from catmaid.control.authentication import requires_user_role
+# from catmaid.control.authentication import requires_user_role
 from catmaid.control.common import get_request_list
 from synapsesuggestor.models import ProjectSynapseSuggestionWorkflow
-from synapsesuggestor.control.common import list_into_query, get_most_recent_project_SS_workflow, \
-    get_project_SS_workflow, get_translation_resolution
+from synapsesuggestor.control.common import (
+    list_into_query, get_most_recent_project_SS_workflow, get_translation_resolution,  # get_project_SS_workflow
+)
 
 
 logger = logging.getLogger(__name__)
 
+
 @api_view(['POST'])
 def add_treenode_synapse_associations(request, project_id=None):
     """
@@ -142,11 +144,11 @@ def get_synapse_objects_info(translation, resolution, synapse_object_ids, cursor
 
     cursor.execute('''
         SELECT combined.so_id, combined.ss_ids, combined.comb_geom
-        FROM (SELECT 
-          three_d.so_id AS so_id, 
-          array_agg(three_d.ss_id) AS ss_ids, 
+        FROM (SELECT
+          three_d.so_id AS so_id,
+          array_agg(three_d.ss_id) AS ss_ids,
           ST_3DUnion(three_d.ss_geom3d) AS comb_geom
-          FROM (SELECT 
+          FROM (SELECT
             ss_so.synapse_object_id AS so_id,
             ss.id AS ss_id,
             ST_Extrude(
@@ -165,8 +167,7 @@ def get_synapse_objects_info(translation, resolution, synapse_object_ids, cursor
             ON ss.synapse_detection_tile_id = tile.id
           WHERE ss_so.id = ANY(%s)) three_d
           GROUP BY three_d.so_id) combined
-    ''',
-       (
+    ''', (
            resolution[0], resolution[1],
            translation[0], translation[1], translation[2], resolution[2],
            synapse_object_ids
@@ -217,7 +218,7 @@ def get_synapse_slices_near_skeletons(request, project_id=None):
     if dimensions == 2:
 
         cursor.execute('''
-            SELECT tn.skeleton_id, tn.id, ss_so2.synapse_object_id, array_agg(DISTINCT ss2.id), 
+            SELECT tn.skeleton_id, tn.id, ss_so2.synapse_object_id, array_agg(DISTINCT ss2.id),
               tile2.z_tile_idx, ARRAY[
                 ST_XMin(ST_Extent(ss2.geom_2d)),
                 ST_YMin(ST_Extent(ss2.geom_2d)),
@@ -231,7 +232,7 @@ def get_synapse_slices_near_skeletons(request, project_id=None):
               ON tile1.z_tile_idx = (tn.location_z / %s) - %s
               AND ST_DWithin(
                     ST_MakePoint((tn.location_x / %s) - %s, (tn.location_y / %s) - %s),
-                    ss1.geom_2d, 
+                    ss1.geom_2d,
                     (%s / %s) - %s
                 )
             INNER JOIN synapse_slice_synapse_object ss_so1

synapsesuggestor/control/workflow.py

@@ -7,7 +7,7 @@
 from django.db import connection
 from rest_framework.decorators import api_view
 
-from catmaid.control.authentication import requires_user_role
+# from catmaid.control.authentication import requires_user_role
 from synapsesuggestor.models import (
     SynapseSuggestionWorkflow, ProjectSynapseSuggestionWorkflow, SynapseDetectionAlgorithm,
     SynapseAssociationAlgorithm, SynapseDetectionTiling
@@ -130,7 +130,9 @@ def _get_valid_workflows(project_id, stack_id):
 #
 #     for row in info:
 #         detection_algos.add((row['detection_algo_hash'], row['detection_algo_date'], row['detection_algo_notes']))
-#         association_algos.add((row['association_algo_hash'], row['association_algo_date'], row['association_algo_notes']))
+#         association_algos.add(
+#             (row['association_algo_hash'], row['association_algo_date'], row['association_algo_notes'])
+#         )
 #         valid_pairs.add((row['detection_algo_hash'], row['association_algo_hash']))
 #
 #     return JsonResponse({

synapsesuggestor/management/commands/drop_ss_tables.py

@@ -6,6 +6,7 @@
 
 from psycopg2.extensions import AsIs
 
+
 class Command(BaseCommand):
     help = 'Closes the specified poll for voting'
 

synapsesuggestor/migrations/0001_initial.py

@@ -102,7 +102,9 @@ class Migration(migrations.Migration):
                 ('xs_centroid', models.IntegerField(verbose_name='x coord of centroid in stack coordinates')),
                 ('ys_centroid', models.IntegerField(verbose_name='y coord of centroid in stack coordinates')),
                 ('uncertainty', models.FloatField(null=True)),
-                ('synapse_detection_tile', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='synapsesuggestor.SynapseDetectionTile')),
+                ('synapse_detection_tile', models.ForeignKey(
+                    on_delete=django.db.models.deletion.CASCADE, to='synapsesuggestor.SynapseDetectionTile'
+                )),
             ],
             options={
                 'db_table': 'synapse_slice',
@@ -112,8 +114,12 @@ class Migration(migrations.Migration):
             name='SynapseSliceSynapseObject',
             fields=[
                 ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('synapse_object', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='synapsesuggestor.SynapseObject')),
-                ('synapse_slice', models.OneToOneField(on_delete=django.db.models.deletion.CASCADE, to='synapsesuggestor.SynapseSlice')),
+                ('synapse_object', models.ForeignKey(
+                    on_delete=django.db.models.deletion.CASCADE, to='synapsesuggestor.SynapseObject'
+                )),
+                ('synapse_slice', models.OneToOneField(
+                    on_delete=django.db.models.deletion.CASCADE, to='synapsesuggestor.SynapseSlice'
+                )),
             ],
             options={
                 'db_table': 'synapse_slice_synapse_object',
@@ -123,10 +129,18 @@ class Migration(migrations.Migration):
             name='SynapseSliceTreenode',
             fields=[
                 ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('contact_px', models.IntegerField(verbose_name='Size in pixels of 1D contact area between neuron and synapse')),
-                ('project_synapse_suggestion_workflow', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='synapsesuggestor.ProjectSynapseSuggestionWorkflow')),
-                ('synapse_slice', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='synapsesuggestor.SynapseSlice')),
-                ('treenode', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='catmaid.Treenode')),
+                ('contact_px', models.IntegerField(
+                    verbose_name='Size in pixels of 1D contact area between neuron and synapse'
+                )),
+                ('project_synapse_suggestion_workflow', models.ForeignKey(
+                    on_delete=django.db.models.deletion.CASCADE, to='synapsesuggestor.ProjectSynapseSuggestionWorkflow'
+                )),
+                ('synapse_slice', models.ForeignKey(
+                    null=True, on_delete=django.db.models.deletion.CASCADE, to='synapsesuggestor.SynapseSlice'
+                )),
+                ('treenode', models.ForeignKey(
+                    null=True, on_delete=django.db.models.deletion.CASCADE, to='catmaid.Treenode'
+                )),
             ],
             options={
                 'db_table': 'synapse_slice_treenode',
@@ -136,9 +150,16 @@ class Migration(migrations.Migration):
             name='SynapseSuggestionWorkflow',
             fields=[
                 ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
-                ('synapse_detection_algorithm', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='synapsesuggestor.SynapseDetectionAlgorithm')),
-                ('synapse_detection_tiling', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='synapsesuggestor.SynapseDetectionTiling')),
-                ('synapse_image_store', models.OneToOneField(default=None, null=True, on_delete=django.db.models.deletion.CASCADE, to='synapsesuggestor.SynapseImageStore')),
+                ('synapse_detection_algorithm', models.ForeignKey(
+                    on_delete=django.db.models.deletion.CASCADE, to='synapsesuggestor.SynapseDetectionAlgorithm'
+                )),
+                ('synapse_detection_tiling', models.ForeignKey(
+                    on_delete=django.db.models.deletion.CASCADE, to='synapsesuggestor.SynapseDetectionTiling'
+                )),
+                ('synapse_image_store', models.OneToOneField(
+                    default=None, null=True, on_delete=django.db.models.deletion.CASCADE,
+                    to='synapsesuggestor.SynapseImageStore'
+                )),
             ],
             options={
                 'db_table': 'synapse_suggestion_workflow',
@@ -147,17 +168,23 @@ class Migration(migrations.Migration):
         migrations.AddField(
             model_name='synapsedetectiontile',
             name='synapse_suggestion_workflow',
-            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='synapsesuggestor.SynapseSuggestionWorkflow'),
+            field=models.ForeignKey(
+                on_delete=django.db.models.deletion.CASCADE, to='synapsesuggestor.SynapseSuggestionWorkflow'
+            ),
         ),
         migrations.AddField(
             model_name='projectsynapsesuggestionworkflow',
             name='synapse_association_algorithm',
-            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='synapsesuggestor.SynapseAssociationAlgorithm'),
+            field=models.ForeignKey(
+                on_delete=django.db.models.deletion.CASCADE, to='synapsesuggestor.SynapseAssociationAlgorithm'
+            ),
         ),
         migrations.AddField(
             model_name='projectsynapsesuggestionworkflow',
             name='synapse_suggestion_workflow',
-            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='synapsesuggestor.SynapseSuggestionWorkflow'),
+            field=models.ForeignKey(
+                on_delete=django.db.models.deletion.CASCADE, to='synapsesuggestor.SynapseSuggestionWorkflow'
+            ),
         ),
         migrations.AlterUniqueTogether(
             name='synapsesuggestionworkflow',

synapsesuggestor/models.py

@@ -5,7 +5,7 @@
 from django.contrib.gis.db import models as spatial_models
 from django.utils.encoding import python_2_unicode_compatible
 
-from catmaid.models import Treenode, Stack, StackMirror, Project
+from catmaid.models import Treenode, Stack, Project
 
 
 @python_2_unicode_compatible

synapsesuggestor/static/synapsesuggestor/js/widgets/synapse-detection-table.js

@@ -659,7 +659,7 @@
    * @param stop
    * @param count
    * @param round
-   * @return {[*]}
+   * @return {Array.<number>}
    */
   const linspace = function(start, stop, count, round) {
     const out = [start];

synapsesuggestor/tests/apis/test_analysis.py

@@ -93,7 +93,7 @@ def create_treenode_connector(
             confidence=confidence
         )
 
-        created_links = create_connector_link(
+        create_connector_link(
             project_id, self.test_user.id, new_treenode.treenode_id, new_treenode.skeleton_id,
             [[new_connector.id, relation.id, confidence]]
         )
@@ -116,8 +116,6 @@ def get_intersecting_connectors(self, obj_ids=None, workflow_id=None):
         self.assertEqual(response.status_code, 200)
         parsed_response = json.loads(response.content.decode('utf-8'))
 
-        print(parsed_response)
-
         if parsed_response['data']:
             self.assertEqual(len(parsed_response['columns']), len(parsed_response['data'][0]))
 

synapsesuggestor/tests/apis/test_synapse_detection.py

@@ -304,8 +304,10 @@ def test_agglomerate_synapse_slices_two_objects(self):
         new_ids = self.insert_synapses(0, (0, 1), height=2)
         parsed_response = self.agglomerate_synapses(new_ids)
 
-        self.assertEqual(len(parsed_response['slice_object_mappings']), 4)  # all 4 syn slices are merged
-        self.assertEqual(len(set(parsed_response['slice_object_mappings'].values())), 1)  # they all map to the same synapse object
+        # check all 4 syn slices are merged
+        self.assertEqual(len(parsed_response['slice_object_mappings']), 4)
+        # check they all map to the same synapse object
+        self.assertEqual(len(set(parsed_response['slice_object_mappings'].values())), 1)
 
         # test old mapping was cleared up
         mappings = SynapseSliceSynapseObject.objects.all()

synapsesuggestor/tests/apis/test_treenode_association.py

@@ -8,8 +8,10 @@
 
 URL_PREFIX = '/ext/synapsesuggestor/treenode-association'
 
-SYN_SLICE_NEAR_SKEL_COLS = ['skeleton_id', 'treenode_id', 'synapse_object_id', 'synapse_slice_ids', 'synapse_z_s',
-               'synapse_bounds_s']
+SYN_SLICE_NEAR_SKEL_COLS = [
+    'skeleton_id', 'treenode_id', 'synapse_object_id', 'synapse_slice_ids', 'synapse_z_s', 'synapse_bounds_s'
+]
+
 
 def stack_to_project(translation, resolution, coords_s):
     """Convert a dictionary of stack coordinates into a dictionary of project coordinates"""