diff --git a/qim3d/features/_common_features_methods.py b/qim3d/features/_common_features_methods.py
index e69b6cba63867c27cbedeba05999e201917f77b7..d7a6960ece0e120661cf66d3b8ff221bf9131f1f 100644
--- a/qim3d/features/_common_features_methods.py
+++ b/qim3d/features/_common_features_methods.py
@@ -5,7 +5,9 @@ import trimesh
import qim3d
-def volume(obj, **mesh_kwargs) -> float:
+def volume(obj: np.ndarray,
+ **mesh_kwargs
+ ) -> float:
"""
Compute the volume of a 3D volume or mesh.
@@ -49,7 +51,9 @@ def volume(obj, **mesh_kwargs) -> float:
return obj.volume
-def area(obj, **mesh_kwargs) -> float:
+def area(obj: np.ndarray,
+ **mesh_kwargs
+ ) -> float:
"""
Compute the surface area of a 3D volume or mesh.
@@ -92,7 +96,9 @@ def area(obj, **mesh_kwargs) -> float:
return obj.area
-def sphericity(obj, **mesh_kwargs) -> float:
+def sphericity(obj: np.ndarray,
+ **mesh_kwargs
+ ) -> float:
"""
Compute the sphericity of a 3D volume or mesh.
diff --git a/qim3d/filters/_common_filter_methods.py b/qim3d/filters/_common_filter_methods.py
index f2d421979259e1f676a54f5ec9512cf2cb6c364e..bc3bab5bba575ea5e01fb847f29e5f9a79971276 100644
--- a/qim3d/filters/_common_filter_methods.py
+++ b/qim3d/filters/_common_filter_methods.py
@@ -26,7 +26,10 @@ __all__ = [
class FilterBase:
- def __init__(self, dask=False, chunks="auto", *args, **kwargs):
+ def __init__(self,
+ dask: bool = False,
+ chunks: str = "auto",
+ *args, **kwargs):
"""
Base class for image filters.
@@ -40,7 +43,7 @@ class FilterBase:
self.kwargs = kwargs
class Gaussian(FilterBase):
- def __call__(self, input):
+ def __call__(self, input: np.ndarray):
"""
Applies a Gaussian filter to the input.
@@ -54,7 +57,7 @@ class Gaussian(FilterBase):
class Median(FilterBase):
- def __call__(self, input):
+ def __call__(self, input: np.ndarray):
"""
Applies a median filter to the input.
@@ -68,7 +71,7 @@ class Median(FilterBase):
class Maximum(FilterBase):
- def __call__(self, input):
+ def __call__(self, input: np.ndarray):
"""
Applies a maximum filter to the input.
@@ -82,7 +85,7 @@ class Maximum(FilterBase):
class Minimum(FilterBase):
- def __call__(self, input):
+ def __call__(self, input: np.ndarray):
"""
Applies a minimum filter to the input.
@@ -95,7 +98,7 @@ class Minimum(FilterBase):
return minimum(input, dask=self.dask, chunks=self.chunks, **self.kwargs)
class Tophat(FilterBase):
- def __call__(self, input):
+ def __call__(self, input: np.ndarray):
"""
Applies a tophat filter to the input.
@@ -210,7 +213,10 @@ class Pipeline:
return input
-def gaussian(vol, dask=False, chunks='auto', *args, **kwargs):
+def gaussian(vol: np.ndarray,
+ dask: bool = False,
+ chunks: str = 'auto',
+ *args, **kwargs) -> np.ndarray:
"""
Applies a Gaussian filter to the input volume using scipy.ndimage.gaussian_filter or dask_image.ndfilters.gaussian_filter.
@@ -236,7 +242,10 @@ def gaussian(vol, dask=False, chunks='auto', *args, **kwargs):
return res
-def median(vol, dask=False, chunks='auto', **kwargs):
+def median(vol: np.ndarray,
+ dask: bool = False,
+ chunks: str ='auto',
+ **kwargs) -> np.ndarray:
"""
Applies a median filter to the input volume using scipy.ndimage.median_filter or dask_image.ndfilters.median_filter.
@@ -260,7 +269,10 @@ def median(vol, dask=False, chunks='auto', **kwargs):
return res
-def maximum(vol, dask=False, chunks='auto', **kwargs):
+def maximum(vol: np.ndarray,
+ dask: bool = False,
+ chunks: str = 'auto',
+ **kwargs) -> np.ndarray:
"""
Applies a maximum filter to the input volume using scipy.ndimage.maximum_filter or dask_image.ndfilters.maximum_filter.
@@ -284,7 +296,10 @@ def maximum(vol, dask=False, chunks='auto', **kwargs):
return res
-def minimum(vol, dask=False, chunks='auto', **kwargs):
+def minimum(vol: np.ndarray,
+ dask: bool = False,
+ chunks: str = 'auto',
+ **kwargs) -> np.ndarray:
"""
Applies a minimum filter to the input volume using scipy.ndimage.minimum_filter or dask_image.ndfilters.minimum_filter.
@@ -307,7 +322,10 @@ def minimum(vol, dask=False, chunks='auto', **kwargs):
res = ndimage.minimum_filter(vol, **kwargs)
return res
-def tophat(vol, dask=False, chunks='auto', **kwargs):
+def tophat(vol: np.ndarray,
+ dask: bool = False,
+ chunks: str = 'auto',
+ **kwargs) -> np.ndarray:
"""
Remove background from the volume.
diff --git a/qim3d/gui/annotation_tool.py b/qim3d/gui/annotation_tool.py
index 4498e1ad2fda3201efec9937d997232ec98db3b5..1ecbc5d30ed5336ab810ae12beb3b1dd655b7ab3 100644
--- a/qim3d/gui/annotation_tool.py
+++ b/qim3d/gui/annotation_tool.py
@@ -36,7 +36,7 @@ from qim3d.gui.interface import BaseInterface
class Interface(BaseInterface):
- def __init__(self, name_suffix: str = "", verbose: bool = False, img=None):
+ def __init__(self, name_suffix: str = "", verbose: bool = False, img: np.ndarray = None):
super().__init__(
title="Annotation Tool",
height=768,
@@ -95,13 +95,13 @@ class Interface(BaseInterface):
except FileNotFoundError:
files = None
- def create_preview(self, img_editor):
+ def create_preview(self, img_editor: gr.ImageEditor):
background = img_editor["background"]
masks = img_editor["layers"][0]
overlay_image = overlay_rgb_images(background, masks)
return overlay_image
- def cerate_download_list(self, img_editor):
+ def cerate_download_list(self, img_editor: gr.ImageEditor):
masks_rgb = img_editor["layers"][0]
mask_threshold = 200 # This value is based
diff --git a/qim3d/gui/interface.py b/qim3d/gui/interface.py
index c559685095cfb69ecf950fcf37e961c7ad0c6bda..0241ce32f382a5168baac77fdcdc70e3efb150e0 100644
--- a/qim3d/gui/interface.py
+++ b/qim3d/gui/interface.py
@@ -48,7 +48,7 @@ class BaseInterface(ABC):
def set_invisible(self):
return gr.update(visible=False)
- def change_visibility(self, is_visible):
+ def change_visibility(self, is_visible: bool):
return gr.update(visible = is_visible)
def launch(self, img=None, force_light_mode: bool = True, **kwargs):
diff --git a/qim3d/gui/iso3d.py b/qim3d/gui/iso3d.py
index 1a20f91ea093a1c65daa0aefd73117445289c588..c7d4620ff1ebdf0df84255cf9a733de047b54d9e 100644
--- a/qim3d/gui/iso3d.py
+++ b/qim3d/gui/iso3d.py
@@ -44,7 +44,7 @@ class Interface(InterfaceWithExamples):
self.img = img
self.plot_height = plot_height
- def load_data(self, gradiofile):
+ def load_data(self, gradiofile: gr.File):
try:
self.vol = load(gradiofile.name)
assert self.vol.ndim == 3
@@ -55,7 +55,7 @@ class Interface(InterfaceWithExamples):
except AssertionError:
raise gr.Error(F"File has to be 3D structure. Your structure has {self.vol.ndim} dimension{'' if self.vol.ndim == 1 else 's'}")
- def resize_vol(self, display_size):
+ def resize_vol(self, display_size: int):
"""Resizes the loaded volume to the display size"""
# Get original size
@@ -80,32 +80,33 @@ class Interface(InterfaceWithExamples):
f"Resized volume: {self.display_size_z, self.display_size_y, self.display_size_x}"
)
- def save_fig(self, fig, filename):
+ def save_fig(self, fig: go.Figure, filename: str):
# Write Plotly figure to disk
fig.write_html(filename)
def create_fig(self,
- gradio_file,
- display_size,
- opacity,
- opacityscale,
- only_wireframe,
- min_value,
- max_value,
- surface_count,
- colormap,
- show_colorbar,
- reversescale,
- flip_z,
- show_axis,
- show_ticks,
- show_caps,
- show_z_slice,
- slice_z_location,
- show_y_slice,
- slice_y_location,
- show_x_slice,
- slice_x_location,):
+ gradio_file: gr.File,
+ display_size: int ,
+ opacity: float,
+ opacityscale: str,
+ only_wireframe: bool,
+ min_value: float,
+ max_value: float,
+ surface_count: int,
+ colormap: str,
+ show_colorbar: bool,
+ reversescale: bool,
+ flip_z: bool,
+ show_axis: bool,
+ show_ticks: bool,
+ show_caps: bool,
+ show_z_slice: bool,
+ slice_z_location: int,
+ show_y_slice: bool,
+ slice_y_location: int,
+ show_x_slice: bool,
+ slice_x_location: int,
+ ) -> tuple[go.Figure, str]:
# Load volume
self.load_data(gradio_file)
diff --git a/qim3d/gui/layers2d.py b/qim3d/gui/layers2d.py
index 780746a093be02faa74d2595538aa4208f2fc056..d3ba41644b3a7b67c294d6e39047f8efcf41324c 100644
--- a/qim3d/gui/layers2d.py
+++ b/qim3d/gui/layers2d.py
@@ -302,14 +302,14 @@ class Interface(BaseInterface):
- def change_plot_type(self, plot_type, ):
+ def change_plot_type(self, plot_type: str, ):
self.plot_type = plot_type
if plot_type == 'Segmentation lines':
return gr.update(visible = False), gr.update(visible = True)
else:
return gr.update(visible = True), gr.update(visible = False)
- def change_plot_size(self, x_check, y_check, z_check):
+ def change_plot_size(self, x_check: int, y_check: int, z_check: int):
"""
Based on how many plots are we displaying (controlled by checkboxes in the bottom) we define
also their height because gradio doesn't do it automatically. The values of heights were set just by eye.
@@ -319,10 +319,10 @@ class Interface(BaseInterface):
height = self.heights[index] # also used to define heights of plots in the begining
return gr.update(height = height, visible= x_check), gr.update(height = height, visible = y_check), gr.update(height = height, visible = z_check)
- def change_row_visibility(self, x_check, y_check, z_check):
+ def change_row_visibility(self, x_check: int, y_check: int, z_check: int):
return self.change_visibility(x_check), self.change_visibility(y_check), self.change_visibility(z_check)
- def update_explorer(self, new_path):
+ def update_explorer(self, new_path: str):
# Refresh the file explorer object
new_path = os.path.expanduser(new_path)
@@ -341,13 +341,13 @@ class Interface(BaseInterface):
def set_relaunch_button(self):
return gr.update(value=f"Relaunch", interactive=True)
- def set_spinner(self, message):
+ def set_spinner(self, message: str):
if self.error:
return gr.Button()
# spinner icon/shows the user something is happeing
return gr.update(value=f"{message}", interactive=False)
- def load_data(self, base_path, explorer):
+ def load_data(self, base_path: str, explorer: str):
if base_path and os.path.isfile(base_path):
file_path = base_path
elif explorer and os.path.isfile(explorer):
diff --git a/qim3d/gui/local_thickness.py b/qim3d/gui/local_thickness.py
index 0c76f1aad4181b5e23d5e2e054009075778f71e4..ad837b42934ac8fa49477cf19773517ccbdbede9 100644
--- a/qim3d/gui/local_thickness.py
+++ b/qim3d/gui/local_thickness.py
@@ -248,7 +248,7 @@ class Interface(InterfaceWithExamples):
#
#######################################################
- def process_input(self, data, dark_objects):
+ def process_input(self, data: np.ndarray, dark_objects: bool):
# Load volume
try:
self.vol = load(data.name)
@@ -265,7 +265,7 @@ class Interface(InterfaceWithExamples):
self.vmin = np.min(self.vol)
self.vmax = np.max(self.vol)
- def show_slice(self, vol, zpos, vmin=None, vmax=None, cmap="viridis"):
+ def show_slice(self, vol: np.ndarray, zpos: int, vmin: float = None, vmax: float = None, cmap: str = "viridis"):
plt.close()
z_idx = int(zpos * (vol.shape[0] - 1))
fig, ax = plt.subplots(figsize=(self.figsize, self.figsize))
@@ -278,19 +278,19 @@ class Interface(InterfaceWithExamples):
return fig
- def make_binary(self, threshold):
+ def make_binary(self, threshold: float):
# Make a binary volume
# Nothing fancy, but we could add new features here
self.vol_binary = self.vol > (threshold * np.max(self.vol))
- def compute_localthickness(self, lt_scale):
+ def compute_localthickness(self, lt_scale: float):
self.vol_thickness = lt.local_thickness(self.vol_binary, lt_scale)
# Valus for visualization
self.vmin_lt = np.min(self.vol_thickness)
self.vmax_lt = np.max(self.vol_thickness)
- def thickness_histogram(self, nbins):
+ def thickness_histogram(self, nbins: int):
# Ignore zero thickness
non_zero_values = self.vol_thickness[self.vol_thickness > 0]
diff --git a/qim3d/gui/qim_theme.py b/qim3d/gui/qim_theme.py
index f13594e4c03bcac851d4e5416e8675cd3fd5f837..5cdc844b695a0fb64e6ff6588ea6b48f0115088e 100644
--- a/qim3d/gui/qim_theme.py
+++ b/qim3d/gui/qim_theme.py
@@ -7,7 +7,7 @@ class QimTheme(gr.themes.Default):
there is a possibility to add some more css if you override _get_css_theme function as shown at the bottom
in comments.
"""
- def __init__(self, force_light_mode:bool = True):
+ def __init__(self, force_light_mode: bool = True):
"""
Parameters:
-----------
diff --git a/qim3d/io/_ome_zarr.py b/qim3d/io/_ome_zarr.py
index ae5173157927dbf4555b05b3a9bacc53f193380a..46b6801c697205bf02846775161fd7e5d9ee1c0e 100644
--- a/qim3d/io/_ome_zarr.py
+++ b/qim3d/io/_ome_zarr.py
@@ -181,16 +181,16 @@ class OMEScaler(
def export_ome_zarr(
- path,
- data,
- chunk_size=256,
- downsample_rate=2,
- order=1,
- replace=False,
- method="scaleZYX",
+ path: str,
+ data: np.ndarray,
+ chunk_size: int = 256,
+ downsample_rate: int = 2,
+ order: int = 1,
+ replace: bool = False,
+ method: str = "scaleZYX",
progress_bar: bool = True,
- progress_bar_repeat_time="auto",
-):
+ progress_bar_repeat_time: str = "auto",
+) -> None:
"""
Export 3D image data to OME-Zarr format with pyramidal downsampling.
@@ -299,7 +299,11 @@ def export_ome_zarr(
return
-def import_ome_zarr(path, scale=0, load=True):
+def import_ome_zarr(
+ path: str,
+ scale: int = 0,
+ load: bool = True
+ ) -> np.ndarray:
"""
Import image data from an OME-Zarr file.
diff --git a/qim3d/io/_saving.py b/qim3d/io/_saving.py
index d7721ee2a082a0a7db3f993c58ec9207eefcc5f4..efe7f2ced024ac5150f27071ea1be1bdeede0dad 100644
--- a/qim3d/io/_saving.py
+++ b/qim3d/io/_saving.py
@@ -401,15 +401,15 @@ class DataSaver:
def save(
- path,
- data,
- replace=False,
- compression=False,
- basename=None,
- sliced_dim=0,
- chunk_shape="auto",
+ path: str,
+ data: np.ndarray,
+ replace: bool = False,
+ compression: bool = False,
+ basename: bool = None,
+ sliced_dim: int = 0,
+ chunk_shape: str = "auto",
**kwargs,
-):
+) -> None:
"""Save data to a specified file path.
Args:
@@ -464,7 +464,10 @@ def save(
).save(path, data)
-def save_mesh(filename, mesh):
+def save_mesh(
+ filename: str,
+ mesh: trimesh.Trimesh
+ ) -> None:
"""
Save a trimesh object to an .obj file.