************* Module recon3d.instance_analysis
src/recon3d/instance_analysis.py:170:0: C0301: Line too long (121/100) (line-too-long)
src/recon3d/instance_analysis.py:171:0: C0301: Line too long (113/100) (line-too-long)
src/recon3d/instance_analysis.py:173:0: C0301: Line too long (135/100) (line-too-long)
src/recon3d/instance_analysis.py:228:0: C0301: Line too long (120/100) (line-too-long)
src/recon3d/instance_analysis.py:229:0: C0301: Line too long (121/100) (line-too-long)
src/recon3d/instance_analysis.py:230:0: C0301: Line too long (113/100) (line-too-long)
src/recon3d/instance_analysis.py:232:0: C0301: Line too long (135/100) (line-too-long)
src/recon3d/instance_analysis.py:267:0: C0301: Line too long (101/100) (line-too-long)
src/recon3d/instance_analysis.py:268:0: C0301: Line too long (101/100) (line-too-long)
src/recon3d/instance_analysis.py:305:0: C0301: Line too long (101/100) (line-too-long)
src/recon3d/instance_analysis.py:306:0: C0301: Line too long (101/100) (line-too-long)
src/recon3d/instance_analysis.py:405:0: C0301: Line too long (117/100) (line-too-long)
src/recon3d/instance_analysis.py:406:0: C0301: Line too long (121/100) (line-too-long)
src/recon3d/instance_analysis.py:407:0: C0301: Line too long (113/100) (line-too-long)
src/recon3d/instance_analysis.py:409:0: C0301: Line too long (562/100) (line-too-long)
src/recon3d/instance_analysis.py:457:0: C0301: Line too long (111/100) (line-too-long)
src/recon3d/instance_analysis.py:613:0: C0301: Line too long (807/100) (line-too-long)
src/recon3d/instance_analysis.py:644:0: C0301: Line too long (124/100) (line-too-long)
src/recon3d/instance_analysis.py:675:0: C0301: Line too long (111/100) (line-too-long)
src/recon3d/instance_analysis.py:676:0: C0301: Line too long (111/100) (line-too-long)
src/recon3d/instance_analysis.py:677:0: C0301: Line too long (110/100) (line-too-long)
src/recon3d/instance_analysis.py:680:0: C0301: Line too long (275/100) (line-too-long)
src/recon3d/instance_analysis.py:788:0: C0301: Line too long (102/100) (line-too-long)
src/recon3d/instance_analysis.py:854:0: C0301: Line too long (107/100) (line-too-long)
src/recon3d/instance_analysis.py:982:0: C0301: Line too long (586/100) (line-too-long)
src/recon3d/instance_analysis.py:1111:0: C0301: Line too long (2574/100) (line-too-long)
src/recon3d/instance_analysis.py:1207:0: C0301: Line too long (108/100) (line-too-long)
src/recon3d/instance_analysis.py:1312:0: C0301: Line too long (102/100) (line-too-long)
src/recon3d/instance_analysis.py:1313:0: C0301: Line too long (106/100) (line-too-long)
src/recon3d/instance_analysis.py:1314:0: C0301: Line too long (108/100) (line-too-long)
src/recon3d/instance_analysis.py:1315:0: C0301: Line too long (106/100) (line-too-long)
src/recon3d/instance_analysis.py:1:0: C0302: Too many lines in module (1342/1000) (too-many-lines)
src/recon3d/instance_analysis.py:12:1: W0511: TODO Integrate with HDF writing (fixme)
src/recon3d/instance_analysis.py:13:1: W0511: TODO Integrate with feature measurements (fixme)
src/recon3d/instance_analysis.py:14:1: W0511: TODO Use constants for Z axis in other module (fixme)
src/recon3d/instance_analysis.py:15:1: W0511: TODO Simplify/Impose structure for image directory (dataset directory in HDF) (fixme)
src/recon3d/instance_analysis.py:17:1: W0511: TODO Devise better solution for multiphase support without if/else blocks (fixme)
src/recon3d/instance_analysis.py:443:5: W0511: TODO: math to account for change in length as function (fixme)
src/recon3d/instance_analysis.py:649:1: W0511: TODO (fixme)
src/recon3d/instance_analysis.py:829:5: W0511: # TODO: test functionality (fixme)
src/recon3d/instance_analysis.py:1011:1: W0511: TODO remove hardcoding here with yml config type (fixme)
src/recon3d/instance_analysis.py:1273:9: W0511: TODO not implemented instance indices yet (fixme)
src/recon3d/instance_analysis.py:25:0: E0401: Unable to import 'h5py' (import-error)
src/recon3d/instance_analysis.py:26:0: E0401: Unable to import 'numpy' (import-error)
src/recon3d/instance_analysis.py:27:0: E0401: Unable to import 'numpy.typing' (import-error)
src/recon3d/instance_analysis.py:29:0: E0401: Unable to import 'PIL' (import-error)
src/recon3d/instance_analysis.py:30:0: E0401: Unable to import 'skimage.io' (import-error)
src/recon3d/instance_analysis.py:31:0: E0401: Unable to import 'sklearn.neighbors' (import-error)
src/recon3d/instance_analysis.py:33:0: E0401: Unable to import 'scipy' (import-error)
src/recon3d/instance_analysis.py:34:0: E0401: Unable to import 'skimage.measure' (import-error)
src/recon3d/instance_analysis.py:35:0: E0401: Unable to import 'cc3d' (import-error)
src/recon3d/instance_analysis.py:36:0: E0401: Unable to import 'fastremap' (import-error)
src/recon3d/instance_analysis.py:42:0: W0401: Wildcard import recon3d.types (wildcard-import)
src/recon3d/instance_analysis.py:73:13: E1136: Value 'np.ndarray' is unsubscriptable (unsubscriptable-object)
src/recon3d/instance_analysis.py:143:13: E1136: Value 'np.ndarray' is unsubscriptable (unsubscriptable-object)
src/recon3d/instance_analysis.py:371:0: R0914: Too many local variables (26/15) (too-many-locals)
src/recon3d/instance_analysis.py:736:0: R0914: Too many local variables (24/15) (too-many-locals)
src/recon3d/instance_analysis.py:1062:0: R0914: Too many local variables (23/15) (too-many-locals)
src/recon3d/instance_analysis.py:1227:4: W0612: Unused variable 'n_semantic_labels' (unused-variable)
src/recon3d/instance_analysis.py:28:0: C0411: standard import "pathlib.Path" should be placed before third party imports "h5py", "numpy", "numpy.typing" (wrong-import-order)
src/recon3d/instance_analysis.py:21:0: W0611: Unused import glob (unused-import)
src/recon3d/instance_analysis.py:22:0: W0611: Unused Final imported from typing (unused-import)
src/recon3d/instance_analysis.py:22:0: W0611: Unused NamedTuple imported from typing (unused-import)
src/recon3d/instance_analysis.py:22:0: W0611: Unused Type imported from typing (unused-import)
src/recon3d/instance_analysis.py:22:0: W0611: Unused List imported from typing (unused-import)
src/recon3d/instance_analysis.py:25:0: W0611: Unused import h5py (unused-import)
src/recon3d/instance_analysis.py:27:0: W0611: Unused numpy.typing imported as npt (unused-import)
src/recon3d/instance_analysis.py:29:0: W0611: Unused Image imported from PIL (unused-import)
src/recon3d/instance_analysis.py:30:0: W0611: Unused skimage.io imported as skio (unused-import)
src/recon3d/instance_analysis.py:33:0: W0611: Unused ndimage imported from scipy (unused-import)
src/recon3d/instance_analysis.py:34:0: W0611: Unused label imported from skimage.measure (unused-import)
src/recon3d/instance_analysis.py:34:0: W0611: Unused regionprops imported from skimage.measure (unused-import)
src/recon3d/instance_analysis.py:42:0: W0614: Unused import(s) npt, CartesianAxis2D, CartesianAxis3D, Angle, EquivalentSphereDiameters, ImageStack, VoidDescriptorEllipsoidAngles, VoidDescriptorFittingParameters, VoidDescriptorProperties, VoidDescriptorPoreProperties, Enum and IntEnum from wildcard import of recon3d.types (unused-wildcard-import)
************* Module recon3d.static_test_paths
src/recon3d/static_test_paths.py:1:0: C0114: Missing module docstring (missing-module-docstring)
************* Module recon3d.constants
src/recon3d/constants.py:29:0: E0401: Unable to import 'numpy' (import-error)
************* Module recon3d.hdf_io
src/recon3d/hdf_io.py:177:0: C0301: Line too long (109/100) (line-too-long)
src/recon3d/hdf_io.py:223:0: C0301: Line too long (125/100) (line-too-long)
src/recon3d/hdf_io.py:704:0: C0301: Line too long (118/100) (line-too-long)
src/recon3d/hdf_io.py:891:0: C0301: Line too long (117/100) (line-too-long)
src/recon3d/hdf_io.py:893:0: C0301: Line too long (147/100) (line-too-long)
src/recon3d/hdf_io.py:1025:0: C0301: Line too long (113/100) (line-too-long)
src/recon3d/hdf_io.py:1:0: C0302: Too many lines in module (1071/1000) (too-many-lines)
src/recon3d/hdf_io.py:198:21: W0511: compression="gzip", #TODO 4/2/24 compression not allowing read in HDF_View (fixme)
src/recon3d/hdf_io.py:280:5: W0511: TODO 4/2/2024 write metadata as attributes (fixme)
src/recon3d/hdf_io.py:282:5: W0511: TODO 5/7/2024 make metadata strings add to h5 (fixme)
src/recon3d/hdf_io.py:674:5: W0511: TODO: AP, write out as single variable length data instead of (fixme)
src/recon3d/hdf_io.py:704:5: W0511: ): # TODO: why does the instance_indices.labels not return the correct type, instead it provides the ndarray... (fixme)
src/recon3d/hdf_io.py:1015:5: W0511: TODO add alternative to ingest npy data dir (fixme)
src/recon3d/hdf_io.py:76:0: E0401: Unable to import 'numpy' (import-error)
src/recon3d/hdf_io.py:77:0: E0401: Unable to import 'h5py' (import-error)
src/recon3d/hdf_io.py:81:0: W0401: Wildcard import recon3d.types (wildcard-import)
src/recon3d/hdf_io.py:117:0: R0913: Too many arguments (6/5) (too-many-arguments)
src/recon3d/hdf_io.py:117:0: R0917: Too many positional arguments (6/5) (too-many-positional-arguments)
src/recon3d/hdf_io.py:191:12: R1705: Unnecessary "else" after "return", remove the "else" and de-indent the code inside it (no-else-return)
src/recon3d/hdf_io.py:209:8: R1705: Unnecessary "elif" after "return", remove the leading "el" from "elif" (no-else-return)
src/recon3d/hdf_io.py:227:0: R1711: Useless return at end of function or method (useless-return)
src/recon3d/hdf_io.py:678:4: W0101: Unreachable code (unreachable)
src/recon3d/hdf_io.py:840:4: W0612: Unused variable 'aa' (unused-variable)
src/recon3d/hdf_io.py:78:0: C0411: standard import "functools.singledispatch" should be placed before third party imports "numpy", "h5py" (wrong-import-order)
src/recon3d/hdf_io.py:81:0: W0614: Unused import(s) npt, CartesianAxis2D, CartesianAxis3D, DataVolume, Units, UnitVector, Angle, Area, InstanceLabels, Length, NVoxel, Volume, Centroid, EllipsoidAxis, EquivalentSphereDiameters, Origin, Resolution, BestFitEllipsoid, MetaData, ImageStack, VoidDescriptorEllipsoidAngles, VoidDescriptorFittingParameters, VoidDescriptorProperties, VoidDescriptorPoreProperties, NamedTuple, Enum and IntEnum from wildcard import of recon3d.types (unused-wildcard-import)
************* Module recon3d.voxel_to_mesh
src/recon3d/voxel_to_mesh.py:219:5: W0511: TODO: Check if the z-order needs to be reveresed based on the CT serial (fixme)
src/recon3d/voxel_to_mesh.py:10:0: E0401: Unable to import 'numpy' (import-error)
src/recon3d/voxel_to_mesh.py:11:0: E0401: Unable to import 'yaml' (import-error)
src/recon3d/voxel_to_mesh.py:14:0: E0401: Unable to import 'automesh' (import-error)
src/recon3d/voxel_to_mesh.py:116:0: R0914: Too many local variables (17/15) (too-many-locals)
src/recon3d/voxel_to_mesh.py:243:11: W0718: Catching too general exception Exception (broad-exception-caught)
src/recon3d/voxel_to_mesh.py:116:0: R0915: Too many statements (56/50) (too-many-statements)
************* Module recon3d.image_stack_to_array
src/recon3d/image_stack_to_array.py:7:0: E0401: Unable to import 'numpy' (import-error)
src/recon3d/image_stack_to_array.py:8:0: E0401: Unable to import 'yaml' (import-error)
src/recon3d/image_stack_to_array.py:49:11: W0718: Catching too general exception Exception (broad-exception-caught)
************* Module recon3d.utility
src/recon3d/utility.py:154:0: C0301: Line too long (102/100) (line-too-long)
src/recon3d/utility.py:174:0: C0301: Line too long (102/100) (line-too-long)
src/recon3d/utility.py:181:0: C0301: Line too long (164/100) (line-too-long)
src/recon3d/utility.py:191:0: C0301: Line too long (104/100) (line-too-long)
src/recon3d/utility.py:192:0: C0301: Line too long (105/100) (line-too-long)
src/recon3d/utility.py:192:0: C0301: Line too long (105/100) (line-too-long)
src/recon3d/utility.py:325:0: C0301: Line too long (114/100) (line-too-long)
src/recon3d/utility.py:326:0: C0301: Line too long (107/100) (line-too-long)
src/recon3d/utility.py:327:0: C0301: Line too long (103/100) (line-too-long)
src/recon3d/utility.py:357:0: C0301: Line too long (114/100) (line-too-long)
src/recon3d/utility.py:358:0: C0301: Line too long (107/100) (line-too-long)
src/recon3d/utility.py:359:0: C0301: Line too long (103/100) (line-too-long)
src/recon3d/utility.py:411:0: C0301: Line too long (1046/100) (line-too-long)
src/recon3d/utility.py:522:0: C0301: Line too long (476/100) (line-too-long)
src/recon3d/utility.py:586:0: C0301: Line too long (111/100) (line-too-long)
src/recon3d/utility.py:587:0: C0301: Line too long (111/100) (line-too-long)
src/recon3d/utility.py:588:0: C0301: Line too long (110/100) (line-too-long)
src/recon3d/utility.py:631:0: C0301: Line too long (111/100) (line-too-long)
src/recon3d/utility.py:632:0: C0301: Line too long (111/100) (line-too-long)
src/recon3d/utility.py:633:0: C0301: Line too long (110/100) (line-too-long)
src/recon3d/utility.py:636:0: C0301: Line too long (115/100) (line-too-long)
src/recon3d/utility.py:637:0: C0301: Line too long (116/100) (line-too-long)
src/recon3d/utility.py:638:0: C0301: Line too long (110/100) (line-too-long)
src/recon3d/utility.py:752:0: C0301: Line too long (118/100) (line-too-long)
src/recon3d/utility.py:1206:0: C0301: Line too long (104/100) (line-too-long)
src/recon3d/utility.py:1:0: C0302: Too many lines in module (1284/1000) (too-many-lines)
src/recon3d/utility.py:113:5: W0511: TODO remove hardcodes and impart flexibility from here to ut.ndarray_to_img call (fixme)
src/recon3d/utility.py:14:0: E0401: Unable to import 'h5py' (import-error)
src/recon3d/utility.py:15:0: E0401: Unable to import 'numpy' (import-error)
src/recon3d/utility.py:16:0: E0401: Unable to import 'yaml' (import-error)
src/recon3d/utility.py:17:0: E0401: Unable to import 'PIL' (import-error)
src/recon3d/utility.py:18:0: E0401: Unable to import 'scipy' (import-error)
src/recon3d/utility.py:19:0: E0401: Unable to import 'skimage' (import-error)
src/recon3d/utility.py:20:0: E0401: Unable to import 'skimage.io' (import-error)
src/recon3d/utility.py:23:0: W0401: Wildcard import recon3d.types (wildcard-import)
src/recon3d/utility.py:107:4: R1720: Unnecessary "else" after "raise", remove the "else" and de-indent the code inside it (no-else-raise)
src/recon3d/utility.py:310:30: W0612: Unused variable 'params' (unused-variable)
src/recon3d/utility.py:384:0: R0914: Too many local variables (24/15) (too-many-locals)
src/recon3d/utility.py:497:0: R0914: Too many local variables (19/15) (too-many-locals)
src/recon3d/utility.py:606:0: R0914: Too many local variables (16/15) (too-many-locals)
src/recon3d/utility.py:1162:0: R0913: Too many arguments (6/5) (too-many-arguments)
src/recon3d/utility.py:19:0: W0611: Unused import skimage (unused-import)
src/recon3d/utility.py:20:0: W0611: Unused skimage.io imported as skio (unused-import)
src/recon3d/utility.py:23:0: W0614: Unused import(s) npt, CartesianAxis2D, Angle, NthNearestNeighbors, EquivalentSphereDiameters, ImageStack, InstanceImageStack, InstanceIndices, SemanticImageStack, VoidDescriptorEllipsoidAngles, VoidDescriptorFittingParameters, VoidDescriptorProperties, VoidDescriptorPoreProperties, NamedTuple, Enum and IntEnum from wildcard import of recon3d.types (unused-wildcard-import)
************* Module recon3d.grayscale_image_stack_to_segmentation
src/recon3d/grayscale_image_stack_to_segmentation.py:9:0: W0622: Redefining built-in 'filter' (redefined-builtin)
src/recon3d/grayscale_image_stack_to_segmentation.py:8:0: E0401: Unable to import 'numpy' (import-error)
src/recon3d/grayscale_image_stack_to_segmentation.py:9:0: E0401: Unable to import 'skimage.filters' (import-error)
src/recon3d/grayscale_image_stack_to_segmentation.py:10:0: E0401: Unable to import 'yaml' (import-error)
src/recon3d/grayscale_image_stack_to_segmentation.py:106:11: W0718: Catching too general exception Exception (broad-exception-caught)
************* Module recon3d.downscale
src/recon3d/downscale.py:52:0: C0301: Line too long (103/100) (line-too-long)
src/recon3d/downscale.py:92:0: C0301: Line too long (123/100) (line-too-long)
src/recon3d/downscale.py:153:0: C0301: Line too long (138/100) (line-too-long)
src/recon3d/downscale.py:343:0: C0301: Line too long (155/100) (line-too-long)
src/recon3d/downscale.py:111:5: W0511: TODO: check this function with RGB image stack as input (fixme)
src/recon3d/downscale.py:172:33: W0511: TODO should we restrict the dimensions to 3? (fixme)
src/recon3d/downscale.py:181:33: W0511: TODO should we restrict the dimensions to 3 (fixme)
src/recon3d/downscale.py:221:5: W0511: TODO: functionalize and test (fixme)
src/recon3d/downscale.py:228:5: W0511: TODO: functionalize and test (fixme)
src/recon3d/downscale.py:35:0: E0401: Unable to import 'numpy' (import-error)
src/recon3d/downscale.py:36:0: E0401: Unable to import 'scipy' (import-error)
src/recon3d/downscale.py:37:0: E0401: Unable to import 'pyevtk.hl' (import-error)
src/recon3d/downscale.py:113:4: C0103: Variable name "N" doesn't conform to snake_case naming style (invalid-name)
src/recon3d/downscale.py:118:4: W0632: Possible unbalanced tuple unpacking with sequence '()': left side has 6 labels, right side has 0 values (unbalanced-tuple-unpacking)
src/recon3d/downscale.py:123:0: R0914: Too many local variables (30/15) (too-many-locals)
src/recon3d/downscale.py:148:8: R1714: Consider merging these comparisons with 'in' by using 'output_stack_type in ('downscaled', 'bounding_box', 'padded')'. Use a set instead if elements are hashable. (consider-using-in)
************* Module recon3d.types
src/recon3d/types.py:15:0: C0301: Line too long (105/100) (line-too-long)
src/recon3d/types.py:59:0: C0301: Line too long (121/100) (line-too-long)
src/recon3d/types.py:146:0: C0301: Line too long (105/100) (line-too-long)
src/recon3d/types.py:343:0: C0301: Line too long (137/100) (line-too-long)
src/recon3d/types.py:345:0: C0301: Line too long (130/100) (line-too-long)
src/recon3d/types.py:415:0: C0301: Line too long (150/100) (line-too-long)
src/recon3d/types.py:417:0: C0301: Line too long (171/100) (line-too-long)
src/recon3d/types.py:436:0: C0301: Line too long (169/100) (line-too-long)
src/recon3d/types.py:438:0: C0301: Line too long (189/100) (line-too-long)
src/recon3d/types.py:457:0: C0301: Line too long (118/100) (line-too-long)
src/recon3d/types.py:459:0: C0301: Line too long (119/100) (line-too-long)
src/recon3d/types.py:500:0: C0301: Line too long (146/100) (line-too-long)
src/recon3d/types.py:502:0: C0301: Line too long (169/100) (line-too-long)
src/recon3d/types.py:525:0: C0301: Line too long (154/100) (line-too-long)
src/recon3d/types.py:527:0: C0301: Line too long (173/100) (line-too-long)
src/recon3d/types.py:639:0: C0301: Line too long (121/100) (line-too-long)
src/recon3d/types.py:87:0: E0401: Unable to import 'numpy' (import-error)
src/recon3d/types.py:88:0: E0401: Unable to import 'numpy.typing' (import-error)
src/recon3d/types.py:300:10: E1136: Value 'np.ndarray' is unsubscriptable (unsubscriptable-object)
src/recon3d/types.py:350:17: E1136: Value 'np.ndarray' is unsubscriptable (unsubscriptable-object)
src/recon3d/types.py:678:18: E1136: Value 'np.ndarray' is unsubscriptable (unsubscriptable-object)
src/recon3d/types.py:1:0: R0801: Similar lines in 2 files
==recon3d.grayscale_image_stack_to_segmentation:[131:162]
==recon3d.image_stack_to_array:[112:143]
print(f"This is {Path(__file__).resolve()}")
fin = yml_input_file.resolve().expanduser()
print(f"Processing file: {fin}")
if not fin.is_file():
raise FileNotFoundError(f"File not found: {str(fin)}")
file_type = fin.suffix.casefold()
supported_types = (".yaml", ".yml")
if file_type not in supported_types:
raise TypeError("Only file types .yaml, and .yml are supported.")
db = []
try:
with open(file=fin, mode="r", encoding="utf-8") as stream:
db = yaml.load(stream, Loader=yaml.SafeLoader) # overwrite
except yaml.YAMLError as error:
print(f"Error with yml module: {error}")
print(f"Could not open or decode: {fin}")
raise OSError from error
print(f"Success: database created from file: {fin}")
print(db)
recipe = Recipe(
image_dir=Path(db["image_dir"]).expanduser(),
image_type=db["image_type"], (duplicate-code)
src/recon3d/types.py:1:0: R0801: Similar lines in 2 files
==recon3d.image_stack_to_array:[87:140]
==recon3d.voxel_to_mesh:[112:172]
return True
def image_to_stack_array(*, yml_input_file: Path) -> bool:
"""Converts a series of images to a stack array.
Parameters
----------
yml_input_file : Path
The path to the input .yml file containing the image paths and other
parameters.
Returns
-------
True if the conversion is successful, False otherwise.
Raises
------
FileNotFoundError
If the input .yml file is not found.
TypeError
If the input file type is not supported.
OSError
If there is an error with the yml module.
"""
print(f"This is {Path(__file__).resolve()}")
fin = yml_input_file.resolve().expanduser()
print(f"Processing file: {fin}")
if not fin.is_file():
raise FileNotFoundError(f"File not found: {str(fin)}")
file_type = fin.suffix.casefold()
supported_types = (".yaml", ".yml")
if file_type not in supported_types:
raise TypeError("Only file types .yaml, and .yml are supported.")
db = []
try:
with open(file=fin, mode="r", encoding="utf-8") as stream:
db = yaml.load(stream, Loader=yaml.SafeLoader) # overwrite
except yaml.YAMLError as error:
print(f"Error with yml module: {error}")
print(f"Could not open or decode: {fin}")
raise OSError from error
print(f"Success: database created from file: {fin}")
print(db)
(duplicate-code)
src/recon3d/types.py:1:0: R0801: Similar lines in 2 files
==recon3d.grayscale_image_stack_to_segmentation:[131:159]
==recon3d.voxel_to_mesh:[144:172]
print(f"This is {Path(__file__).resolve()}")
fin = yml_input_file.resolve().expanduser()
print(f"Processing file: {fin}")
if not fin.is_file():
raise FileNotFoundError(f"File not found: {str(fin)}")
file_type = fin.suffix.casefold()
supported_types = (".yaml", ".yml")
if file_type not in supported_types:
raise TypeError("Only file types .yaml, and .yml are supported.")
db = []
try:
with open(file=fin, mode="r", encoding="utf-8") as stream:
db = yaml.load(stream, Loader=yaml.SafeLoader) # overwrite
except yaml.YAMLError as error:
print(f"Error with yml module: {error}")
print(f"Could not open or decode: {fin}")
raise OSError from error
print(f"Success: database created from file: {fin}")
print(db)
(duplicate-code)
src/recon3d/types.py:1:0: R0801: Similar lines in 2 files
==recon3d.grayscale_image_stack_to_segmentation:[52:62]
==recon3d.image_stack_to_array:[77:87]
assert isinstance(recipe.image_dir, Path), "image_dir must be a Path object"
assert recipe.image_dir.is_dir(), "image_dir must be a directory"
assert isinstance(recipe.image_type, str), "image_type must be a string"
assert recipe.image_type in [
".tif",
".tiff",
], "image_type must be .tif or .tiff"
assert isinstance(recipe.out_dir, Path), "out_path must be a Path object"
assert recipe.out_dir.is_dir(), "out_path must be a directory"
(duplicate-code)
src/recon3d/types.py:1:0: R0801: Similar lines in 2 files
==recon3d.grayscale_image_stack_to_segmentation:[172:205]
==recon3d.image_stack_to_array:[151:184]
out_dir=recipe.out_dir,
)
return True # success
def main():
"""
Runs the module from the command line.
This function serves as the entry point for terminal-based access to the
module. It uses the argparse library to parse command-line arguments.
Parameters
----------
None
Returns
-------
None
Examples
--------
To run the module, use the following command in the terminal:
$ image_to_stack_array path/to/input.yml
"""
parser = argparse.ArgumentParser()
parser.add_argument("input_file", help="the .yml input file")
args = parser.parse_args()
input_file = args.input_file
input_file = Path(input_file).expanduser()
(duplicate-code)
src/recon3d/types.py:1:0: R0801: Similar lines in 2 files
==recon3d.downscale:[401:431]
==recon3d.instance_analysis:[1304:1335]
return True
def main():
"""
Runs the module from the command line, invoked from pyproject.toml with 'downscale' command.
This function sets up the command line argument parser, parses the input arguments,
and calls the `downscale` function with the provided input file.
Parameters
----------
None
Returns
-------
None
Examples
--------
To run this module from the command line with the 'downscale' command:
$ downscale input_file.yml
"""
parser = argparse.ArgumentParser()
parser.add_argument("input_file", help="the .yml user input file")
args = parser.parse_args()
input_file = args.input_file
(duplicate-code)
src/recon3d/types.py:1:0: R0401: Cyclic import (recon3d.hdf_io -> recon3d.instance_analysis) (cyclic-import)
-----------------------------------
Your code has been rated at 7.00/10