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Improve linting and consistency
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@manthey
manthey committed Dec 1, 2023
1 parent bbb91e2 commit c81f307
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Showing 97 changed files with 526 additions and 400 deletions.
58 changes: 30 additions & 28 deletions histomicstk/annotations_and_masks/annotation_and_mask_utils.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ def get_image_from_htk_response(resp):
response from server request
Returns
--------
-------
Pillow Image object
a pillow Image object of the image
Expand All @@ -42,22 +42,22 @@ def scale_slide_annotations(slide_annotations, sf):
Works in place, but returns slide_annotations anyways.
Parameters
-----------
----------
slide_annotations : list of dicts
response from server request
sf : float
scale factor to multiply coordinates
Returns
---------
-------
list of dicts
"""
if sf == 1.0:
return slide_annotations

for annidx, ann in enumerate(slide_annotations):
for _annidx, ann in enumerate(slide_annotations):
for element in ann['annotation']['elements']:
for key in element.keys():

Expand All @@ -75,7 +75,7 @@ def get_scale_factor_and_appendStr(gc, slide_id, MPP=None, MAG=None):
This also gets the string to append to server request for getting rgb.
Parameters
-----------
----------
gc : Girder client instance
gc should be authoenticated.
slide_id : str
Expand All @@ -90,7 +90,7 @@ def get_scale_factor_and_appendStr(gc, slide_id, MPP=None, MAG=None):
scaling at base (scan) magnification.
Returns
----------
-------
float
how much smaller (0.1 means 10x smaller) is requested image
compared to scan magnification (slide coordinates)
Expand Down Expand Up @@ -126,7 +126,7 @@ def rotate_point_list(point_list, rotation, center=(0, 0)):
... web_client/annotations/rotate.js.
Parameters
-----------
----------
point_list : list of tuples
(x,y) coordinates
Expand All @@ -137,7 +137,7 @@ def rotate_point_list(point_list, rotation, center=(0, 0)):
central point coordinates
Returns
--------
-------
list of tuples
"""
Expand Down Expand Up @@ -165,15 +165,15 @@ def get_rotated_rectangular_coords(
of course is applicable to any rotated rectangular annotation.
Parameters
-----------
----------
roi_center : tuple or list
(x, y) format
roi_width : float
roi_height : float
roi_rotation : float
Returns
--------
-------
dict
includes roi corners (x, y) and bounds
Expand Down Expand Up @@ -201,7 +201,7 @@ def get_rotated_rectangular_coords(
'x_min': roi_corners[:, 0].min(),
'x_max': roi_corners[:, 0].max(),
'y_min': roi_corners[:, 1].min(),
'y_max': roi_corners[:, 1].max()
'y_max': roi_corners[:, 1].max(),
}

return roi_info
Expand All @@ -211,12 +211,12 @@ def get_bboxes_from_slide_annotations(slide_annotations):
"""Given a slide annotation list, gets information on bounding boxes.
Parameters
-----------
----------
slide_annotations : list of dicts
response from server request
Returns
---------
-------
Pandas DataFrame
The columns annidx and elementidx encode the
dict index of annotation document and element, respectively, in the
Expand All @@ -227,7 +227,7 @@ def get_bboxes_from_slide_annotations(slide_annotations):

element_infos = DataFrame(columns=[
'annidx', 'elementidx', 'type', 'group',
'xmin', 'xmax', 'ymin', 'ymax', ])
'xmin', 'xmax', 'ymin', 'ymax'])

for annidx, ann in enumerate(slide_annotations):
for elementidx, element in enumerate(ann['annotation']['elements']):
Expand Down Expand Up @@ -295,7 +295,8 @@ def _get_coords_from_element(element):
(xmin, ymax), (xmin, ymin)], dtype='int32')

else:
raise Exception('Unsupported element type:', element['type'])
msg = 'Unsupported element type:'
raise Exception(msg, element['type'])

return coords

Expand All @@ -315,7 +316,7 @@ def _maybe_crop_polygon(vertices, bounds_polygon):
polygon = bounds_polygon.intersection(elpoly)

if polygon.geom_type in ('Polygon', 'LineString'):
polygons_to_add = [polygon, ]
polygons_to_add = [polygon]
else:
polygons_to_add = [
p for p in polygon if p.geom_type == 'Polygon']
Expand Down Expand Up @@ -415,7 +416,7 @@ def parse_slide_annotations_into_tables(
as polygons for simplicity.
Parameters
-----------
----------
slide_annotations : list of dicts
response from server request
Expand All @@ -436,7 +437,7 @@ def parse_slide_annotations_into_tables(
see cropping_bounds description.
Returns
---------
-------
Pandas DataFrame
Summary of key properties of the annotation documents. It has the
following columns:
Expand Down Expand Up @@ -501,7 +502,7 @@ def __init__(self):
'elementidx', 'element_girder_id',
'type', 'group', 'label', 'color',
'xmin', 'xmax', 'ymin', 'ymax', 'bbox_area',
'coords_x', 'coords_y'
'coords_x', 'coords_y',
])

if cfg.cropping_bounds is not None:
Expand Down Expand Up @@ -533,7 +534,7 @@ def __init__(self):
for key in [
'_modelType', '_version',
'itemId', 'created', 'creatorId',
'public', 'updated', 'updatedId', ]:
'public', 'updated', 'updatedId']:
if key in cfg.ann:
cfg.annotation_infos.loc[annno, key] = cfg.ann[key]

Expand All @@ -558,7 +559,7 @@ def __init__(self):
(cfg.cropping_polygon_vertices is None)) \
or (element['type'] == 'point') \
or (not use_shapely):
all_coords = [coords, ]
all_coords = [coords]
else:
all_coords = _maybe_crop_polygon(coords, bounds_polygon)

Expand All @@ -576,14 +577,14 @@ def np_vec_no_jit_iou(bboxes1, bboxes2):
-iou-in-numpy-and-tensor-flow-4fa16231b63d
Parameters
-----------
----------
bboxes1 : np array
columns encode bounding box corners xmin, ymin, xmax, ymax
bboxes2 : np array
same as bboxes 1
Returns
--------
-------
np array
IoU values for each pair from bboxes1 & bboxes2
Expand Down Expand Up @@ -625,7 +626,7 @@ def get_idxs_for_annots_overlapping_roi_by_bbox(
whether the annotation polygons actually overlap the ROI can be done.
Parameters
-----------
----------
element_infos : pandas DataFrame
result from running get_bboxes_from_slide_annotations()
idx_for_roi : int
Expand All @@ -634,7 +635,7 @@ def get_idxs_for_annots_overlapping_roi_by_bbox(
overlap threshold to be considered within ROI
Returns
--------
-------
list
indices relative to element_infos
Expand All @@ -657,13 +658,13 @@ def create_mask_from_coords(coords):
Source: This is modified from code by Juan Carlos from David Gutman Lab.
Parameters
-----------
----------
coords : np array
must be in the form (e.g. ([x1,y1],[x2,y2],[x3,y3],.....,[xn,yn])),
where xn and yn corresponds to the nth vertex coordinate.
Returns
--------
-------
np array
binary mask
Expand Down Expand Up @@ -706,7 +707,8 @@ def _get_element_mask(elinfo, slide_annotations):
roi_height=element['height'], roi_rotation=element['rotation'])
coords = infoDict['roi_corners']
else:
raise Exception('cannot create mask from point annotation!')
msg = 'cannot create mask from point annotation!'
raise Exception(msg)

mask = create_mask_from_coords(coords)
return coords, mask
Expand Down
8 changes: 4 additions & 4 deletions histomicstk/annotations_and_masks/annotation_database_parser.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -109,7 +109,7 @@ def _add_annotation_docs_to_sqlite(dbcon, annotation_docs, item):
'updatedId': String(),
'groups': String(),
'element_count': Integer(),
'element_details': Integer(), },
'element_details': Integer()},
index=False,
)

Expand All @@ -136,7 +136,7 @@ def _add_annotation_elements_to_sqlite(dbcon, annotation_elements):
'ymax': Integer(),
'bbox_area': Integer(),
'coords_x': String(),
'coords_y': String(), },
'coords_y': String()},
index=False,
)

Expand Down Expand Up @@ -199,7 +199,7 @@ def dump_annotations_workflow(
"""Dump annotations for single slide into the local folder.
Parameters
-----------
----------
gc : girder_client.GirderClient
authenticated girder client instance
Expand Down Expand Up @@ -285,7 +285,7 @@ def dump_annotations_locally(
annotations there. Adapted from Lee A.D. Cooper
Parameters
-----------
----------
gc : girder_client.GirderClient
authenticated girder client instance
Expand Down
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