fix flake8 issue

omero/analysis_scripts/Kymograph.py

@@ -175,9 +175,9 @@ def plane_gen():
                 line_data = []
                 points = shape['points']
                 the_z = shape['theZ']
-                for l in range(len(points)-1):
-                    x1, y1 = points[l]
-                    x2, y2 = points[l+1]
+                for point in range(len(points)-1):
+                    x1, y1 = points[point]
+                    x2, y2 = points[point+1]
                     ld = get_line_data(image, x1, y1, x2, y2,
                                        line_width, the_z, the_c, the_t)
                     line_data.append(ld)
@@ -334,15 +334,15 @@ def process_images(conn, script_params):
                     z = the_z
                 # TODO: Add some filter of shapes. E.g. text? / 'lines' only
                 # etc.
-                if type(s) == omero.model.LineI:
+                if isinstance(s, omero.model.LineI):
                     x1 = s.getX1().getValue()
                     x2 = s.getX2().getValue()
                     y1 = s.getY1().getValue()
                     y2 = s.getY2().getValue()
                     lines[t] = {'theZ': z, 'x1': x1, 'y1': y1, 'x2': x2,
                                 'y2': y2}
 
-                elif type(s) == omero.model.PolylineI:
+                elif isinstance(s, omero.model.PolylineI):
                     v = s.getPoints().getValue()
                     points = roi_utils.points_string_to_xy_list(v)
                     polylines[t] = {'theZ': z, 'points': points}

omero/analysis_scripts/Kymograph_Analysis.py

@@ -86,7 +86,7 @@ def process_images(conn, script_params):
             for s in roi.copyShapes():
                 if s is None:
                     continue    # seems possible in some situations
-                if type(s) == omero.model.LineI:
+                if isinstance(s, omero.model.LineI):
                     table_data += "\nLine ID: %s" % s.getId().getValue()
                     x1 = s.getX1().getValue()
                     x2 = s.getX2().getValue()
@@ -103,7 +103,7 @@ def process_images(conn, script_params):
                         [str(x) for x in (y1, x1, y2, x2, dy, dx, dx_per_y,
                                           speed)])
 
-                elif type(s) == omero.model.PolylineI:
+                elif isinstance(s, omero.model.PolylineI):
                     table_data += "\nPolyline ID: %s" % s.getId().getValue()
                     v = s.getPoints().getValue()
                     points = roi_utils.points_string_to_xy_list(v)

omero/analysis_scripts/Plot_Profile.py

@@ -57,9 +57,9 @@ def process_polylines(conn, script_params, image, polylines, line_width, fout):
         points = pl['points']
         for the_c in the_cs:
             ldata = []
-            for l in range(len(points)-1):
-                x1, y1 = points[l]
-                x2, y2 = points[l+1]
+            for point in range(len(points)-1):
+                x1, y1 = points[point]
+                x2, y2 = points[point+1]
                 if round(x1 - x2) == 0 and round(y1 - y2) == 0:
                     continue
                 ld = roi_utils.get_line_data(
@@ -103,11 +103,11 @@ def process_lines(conn, script_params, image, lines, line_width, fout):
     pixels = image.getPrimaryPixels()
     the_cs = script_params['Channels']
 
-    for l in lines:
-        the_t = l['theT']
-        the_z = l['theZ']
-        roi_id = l['id']
-        if round(l['x1'] - l['x2']) == 0 and round(l['y1'] - l['y2']) == 0:
+    for line in lines:
+        the_t = line['theT']
+        the_z = line['theZ']
+        roi_id = line['id']
+        if round(line['x1'] - line['x2']) == 0 and round(line['y1'] - line['y2']) == 0:
             continue
         for the_c in the_cs:
             line_data = []
@@ -192,15 +192,15 @@ def process_images(conn, script_params):
                     z = the_z
                 # TODO: Add some filter of shapes e.g. text? / 'lines' only
                 # etc.
-                if type(s) == omero.model.LineI:
+                if isinstance(s, omero.model.LineI):
                     x1 = s.getX1().getValue()
                     x2 = s.getX2().getValue()
                     y1 = s.getY1().getValue()
                     y2 = s.getY2().getValue()
                     lines.append({'id': roi_id, 'theT': t, 'theZ': z,
                                   'x1': x1, 'y1': y1, 'x2': x2, 'y2': y2})
 
-                elif type(s) == omero.model.PolylineI:
+                elif isinstance(s, omero.model.PolylineI):
                     v = s.getPoints().getValue()
                     points = roi_utils.points_string_to_xy_list(v)
                     polylines.append({'id': roi_id, 'theT': t, 'theZ': z,

omero/annotation_scripts/KeyVal_to_csv.py

@@ -39,7 +39,7 @@
 def get_existing_map_annotions(obj):
     ord_dict = OrderedDict()
     for ann in obj.listAnnotations():
-        if(isinstance(ann, omero.gateway.MapAnnotationWrapper)):
+        if isinstance(ann, omero.gateway.MapAnnotationWrapper):
             kvs = ann.getValue()
             for k, v in kvs:
                 if k not in ord_dict:
@@ -152,8 +152,8 @@ def run_script():
 
             # remove the csv if it exists
             for ann in ds.listAnnotations():
-                if(isinstance(ann, omero.gateway.FileAnnotationWrapper)):
-                    if(ann.getFileName() == csv_name):
+                if isinstance(ann, omero.gateway.FileAnnotationWrapper):
+                    if ann.getFileName() == csv_name:
                         # if the name matches delete it
                         try:
                             delete = Delete2(

omero/export_scripts/Make_Movie.py

@@ -486,8 +486,8 @@ def write_movie(command_args, conn):
         c_windows = []
         c_colours = []
         for c in command_args["ChannelsExtended"]:
-            m = re.match('^(?P<i>\d+)(\|(?P<ws>\d+)' +
-                         '\:(?P<we>\d+))?(\$(?P<c>.+))?$', c)
+            m = re.match('^(?P<i>\\d+)(\\|(?P<ws>\\d+)' +
+                         '\\:(?P<we>\\d+))?(\\$(?P<c>.+))?$', c)
             if m is not None:
                 c_range.append(int(m.group('i'))-1)
                 c_windows.append([float(m.group('ws')), float(m.group('we'))])

omero/figure_scripts/Movie_Figure.py

@@ -311,7 +311,7 @@ def add_left_labels(panel_canvas, image_labels, row_index, width, spacer):
 
     labels = image_labels[row_index]
     py = left_text_height - text_gap  # start at bottom
-    for l, label in enumerate(labels):
+    for count, label in enumerate(labels):
         py = py - text_height    # find the top of this row
         w = textdraw.textsize(label, font=font)[0]
         inset = int((left_text_width - w) / 2)

omero/figure_scripts/Movie_ROI_Figure.py

@@ -589,7 +589,7 @@ def get_tags(name, tags_list, pd_list):
         try:
             height = int(h)
         except ValueError:
-            log("Invalid height: %s Using default value" % (str(h), size_y))
+            log("Invalid height: %s Using default value %s" % (str(h), size_y))
 
     log("Image dimensions for all panels (pixels): width: %d  height: %d"
         % (width, height))

omero/figure_scripts/ROI_Split_Figure.py

@@ -320,7 +320,7 @@ def get_rectangle(roi_service, image_id, roi_label):
         roi_count += 1
         # go through all the shapes of the ROI
         for shape in roi.copyShapes():
-            if type(shape) == omero.model.RectangleI:
+            if isinstance(shape, omero.model.RectangleI):
                 the_t = unwrap(shape.getTheT())
                 the_z = unwrap(shape.getTheZ())
                 t = 0
@@ -660,7 +660,7 @@ def get_tags(name, tags_list, pd_list):
         try:
             height = int(h)
         except ValueError:
-            log("Invalid height: %s Using default value" % (str(h), size_y))
+            log("Invalid height: %s Using default value: %d" % (str(h), size_y))
 
     log("Image dimensions for all panels (pixels): width: %d  height: %d"
         % (width, height))

omero/figure_scripts/Split_View_Figure.py

@@ -404,7 +404,7 @@ def make_split_view_figure(conn, pixel_ids, z_start, z_end, split_indexes,
         image_labels.reverse()
         for row in image_labels:
             py = left_text_width - text_gap  # start at bottom
-            for l, label in enumerate(row):
+            for count, label in enumerate(row):
                 py = py - text_height    # find the top of this row
                 w = textdraw.textsize(label, font=font)[0]
                 inset = int((height - w) // 2)

omero/util_scripts/Dataset_To_Plate.py

@@ -63,7 +63,7 @@ def add_images_to_plate(conn, images, plate_id, column, row, remove_from=None):
     for image in images:
         if remove_from is not None:
             links = list(image.getParentLinks(remove_from.id))
-            link_ids = [l.id for l in links]
+            link_ids = [link.id for link in links]
             conn.deleteObjects('DatasetImageLink', link_ids)
     return True
 

omero/util_scripts/Images_From_ROIs.py

@@ -140,7 +140,7 @@ def get_rectangles(conn, image_id):
         # note x and y for every T, to track moving object
         xy_by_time = {}
         for shape in roi.copyShapes():
-            if type(shape) == omero.model.RectangleI:
+            if isinstance(shape, omero.model.RectangleI):
                 # check t range and z range for every rectangle
                 # t and z (and c) for shape is optional
                 # https://www.openmicroscopy.org/site/support/omero5.2/developers/Model/EveryObject.html#shape

omero/util_scripts/Move_Annotations.py

@@ -62,11 +62,11 @@ def move_well_annotations(conn, well, ann_type, remove_anns, ns):
                                              ns=ns, params=params))
 
     # Filter by type
-    old_links = [l for l in old_links
+    old_links = [link for link in old_links
                  if (ann_type is None
                      or (l.child.__class__.__name__ == ann_type))]
 
-    link_ids = [l.id for l in old_links]
+    link_ids = [link.id for link in old_links]
 
     def get_key(ann_link, with_owner=False):
         # We use ann's 'key' to avoid adding duplicate annotations
@@ -76,28 +76,28 @@ def get_key(ann_link, with_owner=False):
 
     links_dict = {}
     # Remove duplicate annotations according to get_key(l)
-    for l in old_links:
-        links_dict[get_key(l, conn.isAdmin())] = l
+    for link in old_links:
+        links_dict[get_key(link, conn.isAdmin())] = link
 
     old_links = links_dict.values()
 
     # Find existing links on Well so we don't try to duplicate them
     existing_well_links = list(conn.getAnnotationLinks('Well', [well.id],
                                                        ns=ns, params=params))
-    existing_well_keys = [get_key(l) for l in existing_well_links]
+    existing_well_keys = [get_key(l) for link in existing_well_links]
 
     new_links = []
-    for l in old_links:
-        if get_key(l) in existing_well_keys:
+    for link in old_links:
+        if get_key(link) in existing_well_keys:
             continue
-        log("    Annotation: %s %s" % (l.child.id.val,
-                                       l.child.__class__.__name__))
+        log("    Annotation: %s %s" % (link.child.id.val,
+                                       link.child.__class__.__name__))
         link = WellAnnotationLinkI()
         link.parent = WellI(well.id, False)
-        link.child = l.child
+        link.child = link.child
         # If Admin, the new link Owner is same as old link Owner
         if conn.isAdmin():
-            owner_id = l.details.owner.id.val
+            owner_id = link.details.owner.id.val
             link.details.owner = ExperimenterI(owner_id, False)
         new_links.append(link)
     try: