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qim3d/io/_convert.py

@@ -21,7 +21,7 @@ class Convert:
         """
         self.chunk_shape = kwargs.get("chunk_shape", (64, 64, 64))
 
-    def convert(self, input_path, output_path):
+    def convert(self, input_path: str, output_path: str):
         def get_file_extension(file_path):
             root, ext = os.path.splitext(file_path)
             if ext in ['.gz', '.bz2', '.xz']:  # handle common compressed extensions
@@ -67,7 +67,7 @@ class Convert:
             else:
                 raise ValueError("Invalid path")
 
-    def convert_tif_to_zarr(self, tif_path, zarr_path):
+    def convert_tif_to_zarr(self, tif_path: str, zarr_path: str):
         """Convert a tiff file to a zarr file
 
         Args:
@@ -97,7 +97,7 @@ class Convert:
 
         return z
 
-    def convert_zarr_to_tif(self, zarr_path, tif_path):
+    def convert_zarr_to_tif(self, zarr_path: str, tif_path: str):
         """Convert a zarr file to a tiff file
 
         Args:
@@ -110,7 +110,7 @@ class Convert:
         z = zarr.open(zarr_path)
         save(tif_path, z)
 
-    def convert_nifti_to_zarr(self, nifti_path, zarr_path):
+    def convert_nifti_to_zarr(self, nifti_path: str, zarr_path: str):
         """Convert a nifti file to a zarr file
 
         Args:
@@ -139,7 +139,7 @@ class Convert:
 
         return z
 
-    def convert_zarr_to_nifti(self, zarr_path, nifti_path, compression=False):
+    def convert_zarr_to_nifti(self, zarr_path: str, nifti_path: str, compression: bool = False):
         """Convert a zarr file to a nifti file
 
         Args:

qim3d/io/_downloader.py

@@ -76,7 +76,7 @@ class Downloader:
             [file_name_n](load_file,optional): Function to download file number n in the given folder.
         """
 
-        def __init__(self, folder):
+        def __init__(self, folder: str):
             files = _extract_names(folder)
 
             for idx, file in enumerate(files):
@@ -88,7 +88,7 @@ class Downloader:
 
                 setattr(self, f'{file_name.split(".")[0]}', self._make_fn(folder, file))
 
-        def _make_fn(self, folder, file):
+        def _make_fn(self, folder: str, file: str):
             """Private method that returns a function. The function downloads the chosen file from the folder.
 
             Args:
@@ -101,7 +101,7 @@ class Downloader:
 
             url_dl = "https://archive.compute.dtu.dk/download/public/projects/viscomp_data_repository"
 
-            def _download(load_file=False, virtual_stack=True):
+            def _download(load_file: bool = False, virtual_stack: bool = True):
                 """Downloads the file and optionally also loads it.
 
                 Args:
@@ -121,7 +121,7 @@ class Downloader:
             return _download
 
 
-def _update_progress(pbar, blocknum, bs):
+def _update_progress(pbar: tqdm, blocknum: int, bs: int):
     """
     Helper function for the ´download_file()´ function. Updates the progress bar.
     """
@@ -129,7 +129,7 @@ def _update_progress(pbar, blocknum, bs):
     pbar.update(blocknum * bs - pbar.n)
 
 
-def _get_file_size(url):
+def _get_file_size(url: str):
     """
     Helper function for the ´download_file()´ function. Finds the size of the file.
     """
@@ -137,7 +137,7 @@ def _get_file_size(url):
     return int(urllib.request.urlopen(url).info().get("Content-Length", -1))
 
 
-def download_file(path, name, file):
+def download_file(path: str, name: str, file: str):
     """Downloads the file from path / name / file.
 
     Args:
@@ -177,7 +177,7 @@ def download_file(path, name, file):
         )
 
 
-def _extract_html(url):
+def _extract_html(url: str):
     """Extracts the html content of a webpage in "utf-8"
 
     Args:
@@ -198,7 +198,7 @@ def _extract_html(url):
     return html_content
 
 
-def _extract_names(name=None):
+def _extract_names(name: str = None):
     """Extracts the names of the folders and files.
 
     Finds the names of either the folders if no name is given,

qim3d/io/_loading.py

@@ -76,7 +76,7 @@ class DataLoader:
         self.dim_order = kwargs.get("dim_order", (2, 1, 0))
         self.PIL_extensions = (".jp2", ".jpg", "jpeg", ".png", "gif", ".bmp", ".webp")
 
-    def load_tiff(self, path):
+    def load_tiff(self, path: str):
         """Load a TIFF file from the specified path.
 
         Args:
@@ -100,7 +100,7 @@ class DataLoader:
 
         return vol
 
-    def load_h5(self, path):
+    def load_h5(self, path: str):
         """Load an HDF5 file from the specified path.
 
         Args:
@@ -183,7 +183,7 @@ class DataLoader:
         else:
             return vol
 
-    def load_tiff_stack(self, path):
+    def load_tiff_stack(self, path: str):
         """Load a stack of TIFF files from the specified path.
 
         Args:
@@ -237,7 +237,7 @@ class DataLoader:
 
         return vol
 
-    def load_txrm(self, path):
+    def load_txrm(self, path: str):
         """Load a TXRM/XRM/TXM file from the specified path.
 
         Args:
@@ -308,7 +308,7 @@ class DataLoader:
         else:
             return vol
 
-    def load_nifti(self, path):
+    def load_nifti(self, path: str):
         """Load a NIfTI file from the specified path.
 
         Args:
@@ -338,7 +338,7 @@ class DataLoader:
         else:
             return vol
 
-    def load_pil(self, path):
+    def load_pil(self, path: str):
         """Load a PIL image from the specified path
 
         Args:
@@ -349,7 +349,7 @@ class DataLoader:
         """
         return np.array(Image.open(path))
 
-    def load_PIL_stack(self, path):
+    def load_PIL_stack(self, path: str):
         """Load a stack of PIL files from the specified path.
 
         Args:
@@ -433,7 +433,7 @@ class DataLoader:
 
       
 
-    def _load_vgi_metadata(self, path):
+    def _load_vgi_metadata(self, path: str):
         """Helper functions that loads metadata from a VGI file
 
         Args:
@@ -482,7 +482,7 @@ class DataLoader:
 
         return meta_data
 
-    def load_vol(self, path):
+    def load_vol(self, path: str):
         """Load a VOL filed based on the VGI metadata file
 
         Args:
@@ -548,7 +548,7 @@ class DataLoader:
         else:
             return vol
 
-    def load_dicom(self, path):
+    def load_dicom(self, path: str):
         """Load a DICOM file
 
         Args:
@@ -563,7 +563,7 @@ class DataLoader:
         else:
             return dcm_data.pixel_array
 
-    def load_dicom_dir(self, path):
+    def load_dicom_dir(self, path: str):
         """Load a directory of DICOM files into a numpy 3d array
 
         Args:
@@ -654,7 +654,7 @@ class DataLoader:
                     message + " Set 'force_load=True' to ignore this error."
                 )
 
-    def load(self, path):
+    def load(self, path: str):
         """
         Load a file or directory based on the given path.
 
@@ -757,14 +757,14 @@ def _get_ole_offsets(ole):
 
 
 def load(
-    path,
-    virtual_stack=False,
-    dataset_name=None,
-    return_metadata=False,
-    contains=None,
+    path: str,
+    virtual_stack: bool = False,
+    dataset_name: bool = None,
+    return_metadata: bool = False,
+    contains: bool = None,
     progress_bar: bool = True,
     force_load: bool = False,
-    dim_order=(2, 1, 0),
+    dim_order: tuple = (2, 1, 0),
     **kwargs,
 ):
     """
@@ -854,7 +854,7 @@ def load(
 
     return data
 
-def load_mesh(filename):
+def load_mesh(filename: str):
     """
     Load a mesh from an .obj file using trimesh.
 

qim3d/io/_ome_zarr.py

@@ -46,13 +46,13 @@ class OMEScaler(
     """Scaler in the style of OME-Zarr.
     This is needed because their current zoom implementation is broken."""
 
-    def __init__(self, order=0, downscale=2, max_layer=5, method="scaleZYXdask"):
+    def __init__(self, order: int = 0, downscale: float = 2, max_layer: int = 5, method: str = "scaleZYXdask"):
         self.order = order
         self.downscale = downscale
         self.max_layer = max_layer
         self.method = method
 
-    def scaleZYX(self, base):
+    def scaleZYX(self, base: dask.array):
         """Downsample using :func:`scipy.ndimage.zoom`."""
         rv = [base]
         log.info(f"- Scale 0: {rv[-1].shape}")
@@ -63,7 +63,7 @@ class OMEScaler(
 
         return list(rv)
 
-    def scaleZYXdask(self, base):
+    def scaleZYXdask(self, base: dask.array):
         """
         Downsample a 3D volume using Dask and scipy.ndimage.zoom.
 

qim3d/io/_saving.py

@@ -76,7 +76,7 @@ class DataSaver:
         self.sliced_dim = kwargs.get("sliced_dim", 0)
         self.chunk_shape = kwargs.get("chunk_shape", "auto")
 
-    def save_tiff(self, path, data):
+    def save_tiff(self, path: str, data: np.ndarray):
         """Save data to a TIFF file to the given path.
 
         Args:
@@ -85,7 +85,7 @@ class DataSaver:
         """
         tifffile.imwrite(path, data, compression=self.compression)
 
-    def save_tiff_stack(self, path, data):
+    def save_tiff_stack(self, path: str, data: np.ndarray):
         """Save data as a TIFF stack containing slices in separate files to the given path.
         The slices will be named according to the basename plus a suffix with a zero-filled
         value corresponding to the slice number
@@ -124,7 +124,7 @@ class DataSaver:
                 f"Total of {no_slices} files saved following the pattern '{pattern_string}'"
             )
 
-    def save_nifti(self, path, data):
+    def save_nifti(self, path: str, data: np.ndarray):
         """Save data to a NIfTI file to the given path.
 
         Args:
@@ -154,7 +154,7 @@ class DataSaver:
         # Save image
         nib.save(img, path)
 
-    def save_vol(self, path, data):
+    def save_vol(self, path: str, data: np.ndarray):
         """Save data to a VOL file to the given path.
 
         Args:
@@ -200,7 +200,7 @@ class DataSaver:
                 "dataset", data=data, compression="gzip" if self.compression else None
             )
 
-    def save_dicom(self, path, data):
+    def save_dicom(self, path: str, data: np.ndarray):
         """Save data to a DICOM file to the given path.
 
         Args:
@@ -255,7 +255,7 @@ class DataSaver:
 
         ds.save_as(path)
 
-    def save_to_zarr(self, path, data):
+    def save_to_zarr(self, path: str, data: np.ndarray):
         """Saves a Dask array to a Zarr array on disk.
 
         Args:
@@ -284,7 +284,7 @@ class DataSaver:
             )
             zarr_array[:] = data
 
-    def save_PIL(self, path, data):
+    def save_PIL(self, path: str, data: np.ndarray):
         """Save data to a PIL file to the given path.
 
         Args:
@@ -303,7 +303,7 @@ class DataSaver:
         # Save image
         img.save(path)
 
-    def save(self, path, data):
+    def save(self, path: str, data: np.ndarray):
         """Save data to the given path.
 
         Args:

qim3d/io/_sync.py

@@ -28,7 +28,7 @@ class Sync:
 
             return False
 
-    def check_destination(self, source, destination, checksum=False, verbose=True):
+    def check_destination(self, source: str, destination: str, checksum: bool = False, verbose: bool = True):
         """Check if all files from 'source' are in 'destination'
 
         This function compares the files in the 'source' directory to those in
@@ -80,7 +80,7 @@ class Sync:
 
         return diff_files
 
-    def compare_dirs(self, source, destination, checksum=False, verbose=True):
+    def compare_dirs(self, source: str, destination: str, checksum: bool = False, verbose: bool = True):
         """Checks whether 'source' and 'destination' directories are synchronized.
 
         This function compares the contents of two directories
@@ -168,7 +168,7 @@ class Sync:
             )
         return
 
-    def count_files_and_dirs(self, path, verbose=True):
+    def count_files_and_dirs(self, path: str, verbose: bool = True):
         """Count the number of files and directories in the given path.
 
         This function recursively counts the number of files and

qim3d/mesh/_common_mesh_methods.py

@@ -8,8 +8,8 @@ from qim3d.utils._logger import log
 def from_volume(
     volume: np.ndarray,
     level: float = None,
-    step_size=1,
-    allow_degenerate=False,
+    step_size: int = 1,
+    allow_degenerate: bool = False,
     padding: Tuple[int, int, int] = (2, 2, 2),
     **kwargs: Any,
 ) -> trimesh.Trimesh: