Merge pull request #214 from jburel/update

Update

.github/workflows/omero_plugin.yml

@@ -23,7 +23,7 @@ jobs:
     env:
       STAGE: scripts
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Checkout omero-test-infra
         uses: actions/checkout@master
         with:

.github/workflows/publish_pypi.yml

@@ -7,8 +7,10 @@ jobs:
     name: Build and publish Python distribution to PyPI
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
       - name: Build a binary wheel and a source tarball
         run: |
           python -mpip install wheel

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(
@@ -103,17 +103,18 @@ 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:  # noqa
             continue
         for the_c in the_cs:
             line_data = []
-            line_data = roi_utils.get_line_data(pixels, l['x1'], l['y1'],
-                                                l['x2'], l['y2'], line_width,
-                                                the_z, the_c, the_t)
+            line_data = roi_utils.get_line_data(pixels, line['x1'], line['y1'],
+                                                line['x2'], line['y2'],
+                                                line_width, the_z, the_c,
+                                                the_t)
 
             if script_params['Sum_or_Average'] == 'Sum':
                 output_data = line_data.sum(axis=0)
@@ -192,15 +193,15 @@ 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/Batch_Image_Export.py

@@ -123,7 +123,7 @@ def save_plane(image, format, c_name, z_range, project_z, t=0, channel=None,
         w, h = plane.size
         fraction = (float(zoom_percent) / 100)
         plane = plane.resize((int(w * fraction), int(h * fraction)),
-                             Image.ANTIALIAS)
+                             Image.LANCZOS)
 
     if format == "PNG":
         img_name = make_image_name(
@@ -572,7 +572,7 @@ def run_script():
         scripts.String(
             "Zoom", grouping="7", values=zoom_percents,
             description="Zoom (jpeg, png or tiff) before saving with"
-            " ANTIALIAS interpolation", default="100%"),
+            " LANCZOS interpolation", default="100%"),
 
         scripts.String(
             "Format", grouping="8",

omero/export_scripts/Make_Movie.py

@@ -355,7 +355,7 @@ def reshape_to_fit(image, size_x, size_y, bg=(0, 0, 0)):
     # scale
     ratio = min(float(size_x) / image_w, float(size_y) / image_h)
     image = image.resize(map(lambda x: int(x*ratio), image.size),
-                         Image.ANTIALIAS)
+                         Image.LANCZOS)
     # paste
     bg = Image.new("RGBA", (size_x, size_y), (0, 0, 0))     # black bg
     ovlpos = (size_x-image.size[0]) / 2, (size_y-image.size[1]) / 2
@@ -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'))])
@@ -594,7 +594,7 @@ def write_movie(command_args, conn):
         movie_name = "%s.%s" % (movie_name, ext)
 
     # spaces etc in file name cause problems
-    movie_name = re.sub("[$&\;|\(\)<>' ]", "", movie_name)
+    movie_name = re.sub("[$&\\;|\\(\\)<>' ]", "", movie_name)
     frames_per_sec = 2
     if "FPS" in command_args:
         frames_per_sec = command_args["FPS"]

omero/figure_scripts/Movie_Figure.py

@@ -192,7 +192,8 @@ def createmovie_figure(conn, pixel_ids, t_indexes, z_start, z_end, width,
         col_count = min(max_col_count, len(rendered_images))
         row_count = int(math.ceil(len(rendered_images) / col_count))
         font = image_utils.get_font(width // 12)
-        font_height = font.getsize("Textq")[1]
+        box = font.getbbox("Textq")
+        font_height = box[3] - box[1]
         canvas_width = ((width + spacer) * col_count) + spacer
         canvas_height = row_count * (spacer // 2 + font_height +
                                      spacer + height)
@@ -211,7 +212,8 @@ def createmovie_figure(conn, pixel_ids, t_indexes, z_start, z_end, width,
             if t_index >= size_t:
                 continue
             time = time_labels[t]
-            text_w = font.getsize(time)[0]
+            box = font.getbbox(time)
+            text_w = box[2] - box[0]
             inset = (width - text_w) // 2
             textdraw = ImageDraw.Draw(canvas)
             textdraw.text((text_x+inset, text_y), time, font=font,
@@ -295,7 +297,8 @@ def add_left_labels(panel_canvas, image_labels, row_index, width, spacer):
     mode = "RGB"
     white = (255, 255, 255)
     font = image_utils.get_font(width/12)
-    text_height = font.getsize("Sampleq")[1]
+    box = font.getbbox("Sampleq")
+    text_height = box[3] - box[1]
     text_gap = spacer / 2
 
     # find max number of labels
@@ -311,9 +314,9 @@ 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]
+        w = textdraw.textlength(label, font=font)
         inset = int((left_text_width - w) / 2)
         textdraw.text((inset, py), label, font=font, fill=(0, 0, 0))
         py = py - text_gap    # add space between rows

omero/figure_scripts/Movie_ROI_Figure.py

@@ -203,7 +203,8 @@ def get_roi_movie_view(re, query_service, pixels, time_shape_map,
             row_count += 1
         col_count = max_columns
     font = image_utils.get_font(font_size)
-    text_height = font.getsize("Textq")[1]
+    box = font.getbbox("Textq")
+    text_height = box[3] - box[1]
     # no spaces around panels
     canvas_width = ((panel_width + spacer) * col_count) - spacer
     row_height = rendered_images[0].size[1] + spacer + text_height
@@ -221,7 +222,8 @@ def get_roi_movie_view(re, query_service, pixels, time_shape_map,
     col = 0
     for i, img in enumerate(rendered_images):
         label = time_labels[i]
-        indent = (panel_width - (font.getsize(label)[0])) // 2
+        box = font.getbbox(label)
+        indent = (panel_width - (box[2] - box[0])) // 2
         draw.text((px+indent, text_y), label, font=font, fill=(0, 0, 0))
         image_utils.paste_image(img, canvas, px, panel_y)
         if col == (col_count - 1):
@@ -381,7 +383,8 @@ def get_split_view(conn, image_ids, pixel_ids, merged_indexes, merged_colours,
     elif width > 200:
         font_size = 16
     font = image_utils.get_font(font_size)
-    text_height = font.getsize("Textq")[1]
+    box = font.getbbox("Textq")
+    text_height = box[3] - box[1]
     max_count = 0
     for row in image_labels:
         max_count = max(max_count, len(row))
@@ -589,7 +592,7 @@ 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

@@ -180,7 +180,7 @@ def get_roi_split_view(re, pixels, z_start, z_end, split_indexes,
                 # hoping that when we zoom, don't zoom fullImage
             if roi_zoom != 1:
                 new_size = (int(roi_width*roi_zoom), int(roi_height*roi_zoom))
-                roi_image = roi_image.resize(new_size, Image.ANTIALIAS)
+                roi_image = roi_image.resize(new_size, Image.LANCZOS)
             rendered_images.append(roi_image)
             panel_width = roi_image.size[0]
             re.setActive(index, False)  # turn the channel off again!
@@ -213,7 +213,7 @@ def get_roi_split_view(re, pixels, z_start, z_end, split_indexes,
 
     if roi_zoom != 1:
         new_size = (int(roi_width*roi_zoom), int(roi_height*roi_zoom))
-        roi_merged_image = roi_merged_image.resize(new_size, Image.ANTIALIAS)
+        roi_merged_image = roi_merged_image.resize(new_size, Image.LANCZOS)
 
     if channel_mismatch:
         log(" WARNING channel mismatch: The current image has fewer channels"
@@ -224,7 +224,8 @@ def get_roi_split_view(re, pixels, z_start, z_end, split_indexes,
 
     # now assemble the roi split-view canvas
     font = image_utils.get_font(fontsize)
-    text_height = font.getsize("Textq")[1]
+    box = font.getbbox("Textq")
+    text_height = box[3] - box[1]
     top_spacer = 0
     if show_top_labels:
         if merged_names:
@@ -247,7 +248,8 @@ def get_roi_split_view(re, pixels, z_start, z_end, split_indexes,
     draw = ImageDraw.Draw(canvas)
     for i, index in enumerate(split_indexes):
         label = channel_names.get(index, index)
-        indent = (panel_width - (font.getsize(label)[0])) // 2
+        box = font.getbbox(label)
+        indent = (panel_width - (box[2] - box[0])) // 2
         # text is coloured if channel is not coloured AND in the merged image
         rgb = (0, 0, 0)
         if index in merged_colours:
@@ -275,12 +277,14 @@ def get_roi_split_view(re, pixels, z_start, z_end, split_indexes,
                     name = channel_names[index]
                 else:
                     name = str(index)
-                comb_text_width = font.getsize(name)[0]
+                box = font.getbbox(name)
+                comb_text_width = box[2] - box[0]
                 inset = int((panel_width - comb_text_width) / 2)
                 draw.text((px + inset, text_y), name, font=font, fill=rgb)
                 text_y = text_y - text_height
         else:
-            comb_text_width = font.getsize("Merged")[0]
+            box = font.getbbox("Merged")
+            comb_text_width = box[2] - box[0]
             inset = int((panel_width - comb_text_width) / 2)
             draw.text((px + inset, text_y), "Merged", font=font,
                       fill=(0, 0, 0))
@@ -320,7 +324,7 @@ 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
@@ -431,7 +435,8 @@ def get_split_view(conn, image_ids, pixel_ids, split_indexes, channel_names,
     elif width > 200:
         fontsize = 16
     font = image_utils.get_font(fontsize)
-    text_height = font.getsize("Textq")[1]
+    box = font.getbbox("Textq")
+    text_height = box[3] - box[1]
     max_count = 0
     for row in image_labels:
         max_count = max(max_count, len(row))
@@ -660,7 +665,7 @@ 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))  # noqa
 
     log("Image dimensions for all panels (pixels): width: %d  height: %d"
         % (width, height))