From 2394f12a35b09cfd90fd31c51362c1c5c070223e Mon Sep 17 00:00:00 2001
From: fima <fima@dtu.dk>
Date: Thu, 12 Dec 2024 14:26:02 +0100
Subject: [PATCH] Refactoring v1.0 prep
---
docs/notebooks/blob_detection.ipynb | 4 +-
docs/notebooks/local_thickness.ipynb | 4 +-
docs/releases.md | 4 +-
qim3d/__init__.py | 29 +-
qim3d/{cli.py => cli/__init__.py} | 2 +-
qim3d/detection/__init__.py | 1 +
.../_common_detection_methods.py} | 4 +-
qim3d/examples/__init__.py | 2 +-
qim3d/features/__init__.py | 1 +
.../_common_features_methods.py} | 4 +-
qim3d/filters/__init__.py | 1 +
.../_common_filter_methods.py} | 6 +-
qim3d/generate/__init__.py | 4 +-
.../{collection_.py => _aggregators.py} | 10 +-
qim3d/generate/{blob_.py => _generators.py} | 12 +-
qim3d/gui/annotation_tool.py | 2 +-
qim3d/gui/data_explorer.py | 6 +-
qim3d/gui/iso3d.py | 2 +-
qim3d/gui/layers2d.py | 2 +-
qim3d/io/__init__.py | 13 +-
qim3d/io/{convert.py => _convert.py} | 4 +-
qim3d/io/{downloader.py => _downloader.py} | 2 +-
qim3d/io/{loading.py => _loading.py} | 8 +-
qim3d/io/{ome_zarr.py => _ome_zarr.py} | 6 +-
qim3d/io/{saving.py => _saving.py} | 4 +-
qim3d/io/{sync.py => _sync.py} | 2 +-
qim3d/mesh/__init__.py | 1 +
.../mesh.py => mesh/_common_mesh_methods.py} | 4 +-
qim3d/ml/__init__.py | 4 +
.../augmentations.py => ml/_augmentations.py} | 0
qim3d/{models/data.py => ml/_data.py} | 2 +-
qim3d/{models/models.py => ml/_ml_utils.py} | 4 +-
qim3d/ml/models/__init__.py | 1 +
qim3d/{models/unet.py => ml/models/_unet.py} | 2 +-
qim3d/models/__init__.py | 4 -
qim3d/operations/__init__.py | 1 +
.../_common_operations_methods.py} | 77 +--
qim3d/processing/__init__.py | 12 +-
qim3d/processing/{layers2d.py => _layers.py} | 0
...ocal_thickness_.py => _local_thickness.py} | 2 +-
...ucture_tensor_.py => _structure_tensor.py} | 4 +-
qim3d/segmentation/__init__.py | 2 +
.../_common_segmentation_methods.py | 72 +++
.../_connected_components.py} | 2 +-
qim3d/tests/__init__.py | 2 +-
.../processing/test_connected_components.py | 2 +-
qim3d/tests/processing/test_filters.py | 2 +-
qim3d/tests/viz/test_img.py | 24 +-
qim3d/utils/__init__.py | 8 +-
qim3d/utils/{cli.py => _cli.py} | 0
qim3d/utils/{doi.py => _doi.py} | 2 +-
qim3d/utils/{logger.py => _logger.py} | 0
qim3d/utils/{misc.py => _misc.py} | 0
qim3d/utils/{ome_zarr.py => _ome_zarr.py} | 0
.../{progress_bar.py => _progress_bar.py} | 2 +-
qim3d/utils/{server.py => _server.py} | 2 +-
qim3d/utils/{system.py => _system.py} | 4 +-
qim3d/viz/__init__.py | 24 +-
qim3d/viz/{cc.py => _cc.py} | 21 +-
.../viz/{explore.py => _data_exploration.py} | 519 ++++++++++--------
qim3d/viz/{detection.py => _detection.py} | 4 +-
qim3d/viz/{k3d.py => _k3d.py} | 40 +-
qim3d/viz/{layers2d.py => _layers2d.py} | 0
...ocal_thickness_.py => _local_thickness.py} | 2 +-
qim3d/viz/{metrics.py => _metrics.py} | 2 +-
qim3d/viz/{preview.py => _preview.py} | 0
...ructure_tensor.py => _structure_tensor.py} | 2 +-
qim3d/viz/colormaps/__init__.py | 2 +
qim3d/viz/colormaps/_qim_colors.py | 24 +
.../_segmentation.py} | 51 +-
qim3d/viz/itk_vtk_viewer/run.py | 2 +-
71 files changed, 562 insertions(+), 512 deletions(-)
rename qim3d/{cli.py => cli/__init__.py} (98%)
create mode 100644 qim3d/detection/__init__.py
rename qim3d/{processing/detection.py => detection/_common_detection_methods.py} (98%)
create mode 100644 qim3d/features/__init__.py
rename qim3d/{processing/features.py => features/_common_features_methods.py} (97%)
create mode 100644 qim3d/filters/__init__.py
rename qim3d/{processing/filters.py => filters/_common_filter_methods.py} (98%)
rename qim3d/generate/{collection_.py => _aggregators.py} (98%)
rename qim3d/generate/{blob_.py => _generators.py} (96%)
rename qim3d/io/{convert.py => _convert.py} (98%)
rename qim3d/io/{downloader.py => _downloader.py} (99%)
rename qim3d/io/{loading.py => _loading.py} (99%)
rename qim3d/io/{ome_zarr.py => _ome_zarr.py} (98%)
rename qim3d/io/{saving.py => _saving.py} (99%)
rename qim3d/io/{sync.py => _sync.py} (99%)
create mode 100644 qim3d/mesh/__init__.py
rename qim3d/{processing/mesh.py => mesh/_common_mesh_methods.py} (98%)
create mode 100644 qim3d/ml/__init__.py
rename qim3d/{models/augmentations.py => ml/_augmentations.py} (100%)
rename qim3d/{models/data.py => ml/_data.py} (99%)
rename qim3d/{models/models.py => ml/_ml_utils.py} (99%)
create mode 100644 qim3d/ml/models/__init__.py
rename qim3d/{models/unet.py => ml/models/_unet.py} (99%)
delete mode 100644 qim3d/models/__init__.py
create mode 100644 qim3d/operations/__init__.py
rename qim3d/{processing/operations.py => operations/_common_operations_methods.py} (76%)
rename qim3d/processing/{layers2d.py => _layers.py} (100%)
rename qim3d/processing/{local_thickness_.py => _local_thickness.py} (99%)
rename qim3d/processing/{structure_tensor_.py => _structure_tensor.py} (98%)
create mode 100644 qim3d/segmentation/__init__.py
create mode 100644 qim3d/segmentation/_common_segmentation_methods.py
rename qim3d/{processing/cc.py => segmentation/_connected_components.py} (98%)
rename qim3d/utils/{cli.py => _cli.py} (100%)
rename qim3d/utils/{doi.py => _doi.py} (98%)
rename qim3d/utils/{logger.py => _logger.py} (100%)
rename qim3d/utils/{misc.py => _misc.py} (100%)
rename qim3d/utils/{ome_zarr.py => _ome_zarr.py} (100%)
rename qim3d/utils/{progress_bar.py => _progress_bar.py} (99%)
rename qim3d/utils/{server.py => _server.py} (98%)
rename qim3d/utils/{system.py => _system.py} (98%)
rename qim3d/viz/{cc.py => _cc.py} (90%)
rename qim3d/viz/{explore.py => _data_exploration.py} (61%)
rename qim3d/viz/{detection.py => _detection.py} (97%)
rename qim3d/viz/{k3d.py => _k3d.py} (85%)
rename qim3d/viz/{layers2d.py => _layers2d.py} (100%)
rename qim3d/viz/{local_thickness_.py => _local_thickness.py} (99%)
rename qim3d/viz/{metrics.py => _metrics.py} (99%)
rename qim3d/viz/{preview.py => _preview.py} (100%)
rename qim3d/viz/{structure_tensor.py => _structure_tensor.py} (99%)
create mode 100644 qim3d/viz/colormaps/__init__.py
create mode 100644 qim3d/viz/colormaps/_qim_colors.py
rename qim3d/viz/{colormaps.py => colormaps/_segmentation.py} (81%)
diff --git a/docs/notebooks/blob_detection.ipynb b/docs/notebooks/blob_detection.ipynb
index 86f6d946..d23662f9 100644
--- a/docs/notebooks/blob_detection.ipynb
+++ b/docs/notebooks/blob_detection.ipynb
@@ -73,13 +73,13 @@
"cement = qim3d.examples.cement_128x128x128\n",
"\n",
"# Visualize slices of the original cement volume\n",
- "qim3d.viz.slices(cement, n_slices = 5, show = True)\n",
+ "qim3d.viz.slices_grid(cement, n_slices = 5, show = True)\n",
"\n",
"# Apply Gaussian filter to the cement volume\n",
"cement_filtered = qim3d.processing.gaussian(cement, sigma = 2)\n",
"\n",
"# Visualize slices of the filtered cement volume\n",
- "qim3d.viz.slices(cement_filtered)"
+ "qim3d.viz.slices_grid(cement_filtered)"
]
},
{
diff --git a/docs/notebooks/local_thickness.ipynb b/docs/notebooks/local_thickness.ipynb
index 717c8546..ee405d83 100644
--- a/docs/notebooks/local_thickness.ipynb
+++ b/docs/notebooks/local_thickness.ipynb
@@ -179,13 +179,13 @@
"cement = qim3d.examples.cement_128x128x128\n",
"\n",
"# Visualize slices of the original cement volume\n",
- "qim3d.viz.slices(cement, n_slices = 5, show = True)\n",
+ "qim3d.viz.slices_grid(cement, n_slices = 5, show = True)\n",
"\n",
"# Apply Gaussian filter to the cement volume\n",
"cement_filtered = qim3d.processing.gaussian(cement, sigma = 2)\n",
"\n",
"# Visualize slices of the filtered cement volume\n",
- "qim3d.viz.slices(cement_filtered)"
+ "qim3d.viz.slices_grid(cement_filtered)"
]
},
{
diff --git a/docs/releases.md b/docs/releases.md
index ff67814f..cee2d6a4 100644
--- a/docs/releases.md
+++ b/docs/releases.md
@@ -114,7 +114,7 @@ This version focus on the increased usability of the `qim3d` library
- Online documentation available at [https://platform.qim.dk/qim3d](https://platform.qim.dk/qim3d)
- Virtual stacks also available for `txm` files
- Updated GUI launch pipeline
-- New functionalities for `qim3d.viz.slices`
+- New functionalities for `qim3d.viz.slices_grid`
- Introduction of `qim3d.processing.filters` 🎉
- Introduction of `qim3d.viz.vol` 🎉
@@ -140,7 +140,7 @@ Includes new develoments toward the usability of the library, as well as its int
- For the local thicknes GUI, now it is possible to pass and receive numpy arrays instead of using the upload functionality.
- Improved data loader
- Now the extensions `tif`, `h5` and `txm` are supported.
-- Added `qim3d.viz.slices` for easy slice visualization.
+- Added `qim3d.viz.slices_grid` for easy slice visualization.
- U-net model creation
- Model availabe from `qim3d.models.UNet`
- Data augmentation class at `qim3d.utils.Augmentation`
diff --git a/qim3d/__init__.py b/qim3d/__init__.py
index 07782e4e..b08fa27c 100644
--- a/qim3d/__init__.py
+++ b/qim3d/__init__.py
@@ -8,7 +8,7 @@ Documentation available at https://platform.qim.dk/qim3d/
"""
-__version__ = "0.4.5"
+__version__ = "0.9.0"
import importlib as _importlib
@@ -33,18 +33,23 @@ class _LazyLoader:
# List of submodules
_submodules = [
- "examples",
- "generate",
- "gui",
- "io",
- "models",
- "processing",
- "tests",
- "utils",
- "viz",
- "cli",
+ 'examples',
+ 'generate',
+ 'gui',
+ 'io',
+ 'ml',
+ 'processing',
+ 'tests',
+ 'utils',
+ 'viz',
+ 'cli',
+ 'filters',
+ 'segmentation',
+ 'mesh',
+ 'features',
+ 'operations',
]
# Creating lazy loaders for each submodule
for submodule in _submodules:
- globals()[submodule] = _LazyLoader(f"qim3d.{submodule}")
+ globals()[submodule] = _LazyLoader(f'qim3d.{submodule}')
diff --git a/qim3d/cli.py b/qim3d/cli/__init__.py
similarity index 98%
rename from qim3d/cli.py
rename to qim3d/cli/__init__.py
index 9f6e1ae0..ef60bdb8 100644
--- a/qim3d/cli.py
+++ b/qim3d/cli/__init__.py
@@ -177,7 +177,7 @@ def main():
elif args.method == "k3d":
volume = qim3d.io.load(str(args.source))
print("\nGenerating k3d plot...")
- qim3d.viz.vol(volume, show=False, save=str(args.destination))
+ qim3d.viz.volumetric(volume, show=False, save=str(args.destination))
print(f"Done, plot available at <{args.destination}>")
if not args.no_browser:
print("Opening in default browser...")
diff --git a/qim3d/detection/__init__.py b/qim3d/detection/__init__.py
new file mode 100644
index 00000000..302d7909
--- /dev/null
+++ b/qim3d/detection/__init__.py
@@ -0,0 +1 @@
+from qim3d.detection._common_detection_methods import *
\ No newline at end of file
diff --git a/qim3d/processing/detection.py b/qim3d/detection/_common_detection_methods.py
similarity index 98%
rename from qim3d/processing/detection.py
rename to qim3d/detection/_common_detection_methods.py
index e3650cf1..ff57026a 100644
--- a/qim3d/processing/detection.py
+++ b/qim3d/detection/_common_detection_methods.py
@@ -1,7 +1,9 @@
""" Blob detection using Difference of Gaussian (DoG) method """
import numpy as np
-from qim3d.utils.logger import log
+from qim3d.utils._logger import log
+
+__all__ = ["blob_detection"]
def blob_detection(
vol: np.ndarray,
diff --git a/qim3d/examples/__init__.py b/qim3d/examples/__init__.py
index cf574696..fe15a92e 100644
--- a/qim3d/examples/__init__.py
+++ b/qim3d/examples/__init__.py
@@ -1,7 +1,7 @@
""" Example images for testing and demonstration purposes. """
from pathlib import Path as _Path
-from qim3d.utils.logger import log as _log
+from qim3d.utils._logger import log as _log
from qim3d.io import load as _load
# Save the original log level and set to ERROR
diff --git a/qim3d/features/__init__.py b/qim3d/features/__init__.py
new file mode 100644
index 00000000..349cedcb
--- /dev/null
+++ b/qim3d/features/__init__.py
@@ -0,0 +1 @@
+from ._common_features_methods import volume, area, sphericity
diff --git a/qim3d/processing/features.py b/qim3d/features/_common_features_methods.py
similarity index 97%
rename from qim3d/processing/features.py
rename to qim3d/features/_common_features_methods.py
index 9dd08702..e69b6cba 100644
--- a/qim3d/processing/features.py
+++ b/qim3d/features/_common_features_methods.py
@@ -1,6 +1,6 @@
import numpy as np
import qim3d.processing
-from qim3d.utils.logger import log
+from qim3d.utils._logger import log
import trimesh
import qim3d
@@ -44,7 +44,7 @@ def volume(obj, **mesh_kwargs) -> float:
"""
if isinstance(obj, np.ndarray):
log.info("Converting volume to mesh.")
- obj = qim3d.processing.create_mesh(obj, **mesh_kwargs)
+ obj = qim3d.mesh.from_volume(obj, **mesh_kwargs)
return obj.volume
diff --git a/qim3d/filters/__init__.py b/qim3d/filters/__init__.py
new file mode 100644
index 00000000..8a166fca
--- /dev/null
+++ b/qim3d/filters/__init__.py
@@ -0,0 +1 @@
+from ._common_filter_methods import *
\ No newline at end of file
diff --git a/qim3d/processing/filters.py b/qim3d/filters/_common_filter_methods.py
similarity index 98%
rename from qim3d/processing/filters.py
rename to qim3d/filters/_common_filter_methods.py
index 3c3c1a5b..f2d42197 100644
--- a/qim3d/processing/filters.py
+++ b/qim3d/filters/_common_filter_methods.py
@@ -8,7 +8,7 @@ from skimage import morphology
import dask.array as da
import dask_image.ndfilters as dask_ndfilters
-from qim3d.utils.logger import log
+from qim3d.utils._logger import log
__all__ = [
"Gaussian",
@@ -119,7 +119,7 @@ class Pipeline:
vol = qim3d.examples.fly_150x256x256
# Show original
- qim3d.viz.slices(vol, axis=0, show=True)
+ qim3d.viz.slices_grid(vol, axis=0, show=True)
# Create filter pipeline
pipeline = Pipeline(
@@ -134,7 +134,7 @@ class Pipeline:
vol_filtered = pipeline(vol)
# Show filtered
- qim3d.viz.slices(vol_filtered, axis=0)
+ qim3d.viz.slices_grid(vol_filtered, axis=0)
```
diff --git a/qim3d/generate/__init__.py b/qim3d/generate/__init__.py
index 6ad08aa7..3f0a4878 100644
--- a/qim3d/generate/__init__.py
+++ b/qim3d/generate/__init__.py
@@ -1,2 +1,2 @@
-from .blob_ import blob
-from .collection_ import collection
\ No newline at end of file
+from ._generators import noise_object
+from ._aggregators import noise_object_collection
diff --git a/qim3d/generate/collection_.py b/qim3d/generate/_aggregators.py
similarity index 98%
rename from qim3d/generate/collection_.py
rename to qim3d/generate/_aggregators.py
index dc54da7e..9d10df37 100644
--- a/qim3d/generate/collection_.py
+++ b/qim3d/generate/_aggregators.py
@@ -3,7 +3,7 @@ import scipy.ndimage
from tqdm.notebook import tqdm
import qim3d.generate
-from qim3d.utils.logger import log
+from qim3d.utils._logger import log
def random_placement(
@@ -120,7 +120,7 @@ def specific_placement(
return collection, placed, positions
-def collection(
+def noise_object_collection(
collection_shape: tuple = (200, 200, 200),
num_objects: int = 15,
positions: list[tuple] = None,
@@ -255,7 +255,7 @@ def collection(
```python
# Visualize slices
- qim3d.viz.slices(vol, n_slices=15)
+ qim3d.viz.slices_grid(vol, n_slices=15)
```
@@ -285,7 +285,7 @@ def collection(
```python
# Visualize slices
- qim3d.viz.slices(vol, n_slices=15, axis=1)
+ qim3d.viz.slices_grid(vol, n_slices=15, axis=1)
```
"""
@@ -350,7 +350,7 @@ def collection(
log.debug(f"- Threshold: {threshold:.3f}")
# Generate synthetic object
- blob = qim3d.generate.blob(
+ blob = qim3d.generate.noise_object(
base_shape=blob_shape,
final_shape=final_shape,
noise_scale=noise_scale,
diff --git a/qim3d/generate/blob_.py b/qim3d/generate/_generators.py
similarity index 96%
rename from qim3d/generate/blob_.py
rename to qim3d/generate/_generators.py
index 153bdcfc..78bf607b 100644
--- a/qim3d/generate/blob_.py
+++ b/qim3d/generate/_generators.py
@@ -4,7 +4,7 @@ from noise import pnoise3
import qim3d.processing
-def blob(
+def noise_object(
base_shape: tuple = (128, 128, 128),
final_shape: tuple = (128, 128, 128),
noise_scale: float = 0.05,
@@ -32,7 +32,7 @@ def blob(
dtype (str, optional): Desired data type of the output volume. Defaults to "uint8".
Returns:
- synthetic_blob (numpy.ndarray): Generated 3D volume with specified parameters.
+ noise_object (numpy.ndarray): Generated 3D volume with specified parameters.
Raises:
TypeError: If `final_shape` is not a tuple or does not have three elements.
@@ -52,7 +52,7 @@ def blob(
```python
# Visualize slices
- qim3d.viz.slices(synthetic_blob, vmin = 0, vmax = 255, n_slices = 15)
+ qim3d.viz.slices_grid(synthetic_blob, vmin = 0, vmax = 255, n_slices = 15)
```
@@ -69,14 +69,14 @@ def blob(
object_shape = "cylinder"
)
- # Visualize synthetic blob
+ # Visualize synthetic object
qim3d.viz.vol(vol)
```
<iframe src="https://platform.qim.dk/k3d/synthetic_blob_cylinder.html" width="100%" height="500" frameborder="0"></iframe>
```python
# Visualize slices
- qim3d.viz.slices(vol, n_slices=15, axis=1)
+ qim3d.viz.slices_grid(vol, n_slices=15, axis=1)
```
@@ -100,7 +100,7 @@ def blob(
```python
# Visualize
- qim3d.viz.slices(vol, n_slices=15)
+ qim3d.viz.slices_grid(vol, n_slices=15)
```
"""
diff --git a/qim3d/gui/annotation_tool.py b/qim3d/gui/annotation_tool.py
index 99863cf4..4498e1ad 100644
--- a/qim3d/gui/annotation_tool.py
+++ b/qim3d/gui/annotation_tool.py
@@ -29,7 +29,7 @@ import numpy as np
from PIL import Image
from qim3d.io import load, save
-from qim3d.processing.operations import overlay_rgb_images
+from qim3d.operations._common_operations_methods import overlay_rgb_images
from qim3d.gui.interface import BaseInterface
# TODO: img in launch should be self.img
diff --git a/qim3d/gui/data_explorer.py b/qim3d/gui/data_explorer.py
index 4d2b1f51..ecabeb81 100644
--- a/qim3d/gui/data_explorer.py
+++ b/qim3d/gui/data_explorer.py
@@ -25,8 +25,8 @@ import numpy as np
import outputformat as ouf
from qim3d.io import load
-from qim3d.utils.logger import log
-from qim3d.utils import misc
+from qim3d.utils._logger import log
+from qim3d.utils import _misc
from qim3d.gui.interface import BaseInterface
@@ -550,7 +550,7 @@ class Interface(BaseInterface):
def show_data_summary(self):
summary_dict = {
"Last modified": datetime.datetime.fromtimestamp(os.path.getmtime(self.file_path)).strftime("%Y-%m-%d %H:%M"),
- "File size": misc.sizeof(os.path.getsize(self.file_path)),
+ "File size": _misc.sizeof(os.path.getsize(self.file_path)),
"Z-size": str(self.vol.shape[self.axis_dict["Z"]]),
"Y-size": str(self.vol.shape[self.axis_dict["Y"]]),
"X-size": str(self.vol.shape[self.axis_dict["X"]]),
diff --git a/qim3d/gui/iso3d.py b/qim3d/gui/iso3d.py
index 16bf8ffe..1a20f91e 100644
--- a/qim3d/gui/iso3d.py
+++ b/qim3d/gui/iso3d.py
@@ -23,7 +23,7 @@ import plotly.graph_objects as go
from scipy import ndimage
from qim3d.io import load
-from qim3d.utils.logger import log
+from qim3d.utils._logger import log
from qim3d.gui.interface import InterfaceWithExamples
diff --git a/qim3d/gui/layers2d.py b/qim3d/gui/layers2d.py
index cf106ded..780746a0 100644
--- a/qim3d/gui/layers2d.py
+++ b/qim3d/gui/layers2d.py
@@ -27,7 +27,7 @@ from .interface import BaseInterface
# from qim3d.processing import layers2d as l2d
from qim3d.processing import overlay_rgb_images, segment_layers, get_lines
from qim3d.io import load
-from qim3d.viz.layers2d import image_with_lines
+from qim3d.viz._layers2d import image_with_lines
#TODO figure out how not update anything and go through processing when there are no data loaded
# So user could play with the widgets but it doesnt throw error
diff --git a/qim3d/io/__init__.py b/qim3d/io/__init__.py
index b56cec9b..84560054 100644
--- a/qim3d/io/__init__.py
+++ b/qim3d/io/__init__.py
@@ -1,7 +1,6 @@
-from .loading import DataLoader, load, load_mesh
-from .downloader import Downloader
-from .saving import DataSaver, save, save_mesh
-from .sync import Sync
-from .convert import convert
-from ..utils import logger
-from .ome_zarr import export_ome_zarr, import_ome_zarr
+from ._loading import load, load_mesh
+from ._downloader import Downloader
+from ._saving import save, save_mesh
+# from ._sync import Sync # this will be added back after future development
+from ._convert import convert
+from ._ome_zarr import export_ome_zarr, import_ome_zarr
diff --git a/qim3d/io/convert.py b/qim3d/io/_convert.py
similarity index 98%
rename from qim3d/io/convert.py
rename to qim3d/io/_convert.py
index 411c35b2..4ab6c0a9 100644
--- a/qim3d/io/convert.py
+++ b/qim3d/io/_convert.py
@@ -8,8 +8,8 @@ import tifffile as tiff
import zarr
from tqdm import tqdm
-from qim3d.utils.misc import stringify_path
-from qim3d.io.saving import save
+from qim3d.utils._misc import stringify_path
+from qim3d.io._saving import save
class Convert:
diff --git a/qim3d/io/downloader.py b/qim3d/io/_downloader.py
similarity index 99%
rename from qim3d/io/downloader.py
rename to qim3d/io/_downloader.py
index c9428492..fe42e410 100644
--- a/qim3d/io/downloader.py
+++ b/qim3d/io/_downloader.py
@@ -8,7 +8,7 @@ from tqdm import tqdm
from pathlib import Path
from qim3d.io import load
-from qim3d.utils.logger import log
+from qim3d.utils._logger import log
import outputformat as ouf
diff --git a/qim3d/io/loading.py b/qim3d/io/_loading.py
similarity index 99%
rename from qim3d/io/loading.py
rename to qim3d/io/_loading.py
index 464bddde..e5f2191e 100644
--- a/qim3d/io/loading.py
+++ b/qim3d/io/_loading.py
@@ -23,10 +23,10 @@ from dask import delayed
from PIL import Image, UnidentifiedImageError
import qim3d
-from qim3d.utils.logger import log
-from qim3d.utils.misc import get_file_size, sizeof, stringify_path
-from qim3d.utils.system import Memory
-from qim3d.utils.progress_bar import FileLoadingProgressBar
+from qim3d.utils._logger import log
+from qim3d.utils._misc import get_file_size, sizeof, stringify_path
+from qim3d.utils._system import Memory
+from qim3d.utils._progress_bar import FileLoadingProgressBar
import trimesh
dask.config.set(scheduler="processes")
diff --git a/qim3d/io/ome_zarr.py b/qim3d/io/_ome_zarr.py
similarity index 98%
rename from qim3d/io/ome_zarr.py
rename to qim3d/io/_ome_zarr.py
index feca0622..ae517315 100644
--- a/qim3d/io/ome_zarr.py
+++ b/qim3d/io/_ome_zarr.py
@@ -31,9 +31,9 @@ from skimage.transform import (
resize,
)
-from qim3d.utils.logger import log
-from qim3d.utils.progress_bar import OmeZarrExportProgressBar
-from qim3d.utils.ome_zarr import get_n_chunks
+from qim3d.utils._logger import log
+from qim3d.utils._progress_bar import OmeZarrExportProgressBar
+from qim3d.utils._ome_zarr import get_n_chunks
ListOfArrayLike = Union[List[da.Array], List[np.ndarray]]
diff --git a/qim3d/io/saving.py b/qim3d/io/_saving.py
similarity index 99%
rename from qim3d/io/saving.py
rename to qim3d/io/_saving.py
index efc2333a..d7721ee2 100644
--- a/qim3d/io/saving.py
+++ b/qim3d/io/_saving.py
@@ -37,8 +37,8 @@ from pydicom.dataset import FileDataset, FileMetaDataset
from pydicom.uid import UID
import trimesh
-from qim3d.utils.logger import log
-from qim3d.utils.misc import sizeof, stringify_path
+from qim3d.utils._logger import log
+from qim3d.utils._misc import sizeof, stringify_path
class DataSaver:
diff --git a/qim3d/io/sync.py b/qim3d/io/_sync.py
similarity index 99%
rename from qim3d/io/sync.py
rename to qim3d/io/_sync.py
index 3992cd33..9085ae88 100644
--- a/qim3d/io/sync.py
+++ b/qim3d/io/_sync.py
@@ -2,7 +2,7 @@
import os
import subprocess
import outputformat as ouf
-from qim3d.utils.logger import log
+from qim3d.utils._logger import log
from pathlib import Path
diff --git a/qim3d/mesh/__init__.py b/qim3d/mesh/__init__.py
new file mode 100644
index 00000000..932dfd9e
--- /dev/null
+++ b/qim3d/mesh/__init__.py
@@ -0,0 +1 @@
+from ._common_mesh_methods import from_volume
diff --git a/qim3d/processing/mesh.py b/qim3d/mesh/_common_mesh_methods.py
similarity index 98%
rename from qim3d/processing/mesh.py
rename to qim3d/mesh/_common_mesh_methods.py
index b4ff6783..535fcae8 100644
--- a/qim3d/processing/mesh.py
+++ b/qim3d/mesh/_common_mesh_methods.py
@@ -2,10 +2,10 @@ import numpy as np
from skimage import measure, filters
import trimesh
from typing import Tuple, Any
-from qim3d.utils.logger import log
+from qim3d.utils._logger import log
-def create_mesh(
+def from_volume(
volume: np.ndarray,
level: float = None,
step_size=1,
diff --git a/qim3d/ml/__init__.py b/qim3d/ml/__init__.py
new file mode 100644
index 00000000..cf15999b
--- /dev/null
+++ b/qim3d/ml/__init__.py
@@ -0,0 +1,4 @@
+from ._augmentations import Augmentation
+from ._data import Dataset, prepare_dataloaders, prepare_datasets
+from ._ml_utils import inference, model_summary, train_model
+from .models import *
\ No newline at end of file
diff --git a/qim3d/models/augmentations.py b/qim3d/ml/_augmentations.py
similarity index 100%
rename from qim3d/models/augmentations.py
rename to qim3d/ml/_augmentations.py
diff --git a/qim3d/models/data.py b/qim3d/ml/_data.py
similarity index 99%
rename from qim3d/models/data.py
rename to qim3d/ml/_data.py
index fc61d262..38fbdac7 100644
--- a/qim3d/models/data.py
+++ b/qim3d/ml/_data.py
@@ -1,7 +1,7 @@
"""Provides a custom Dataset class for building a PyTorch dataset."""
from pathlib import Path
from PIL import Image
-from qim3d.utils.logger import log
+from qim3d.utils._logger import log
import torch
import numpy as np
diff --git a/qim3d/models/models.py b/qim3d/ml/_ml_utils.py
similarity index 99%
rename from qim3d/models/models.py
rename to qim3d/ml/_ml_utils.py
index f0405249..7c8a3b86 100644
--- a/qim3d/models/models.py
+++ b/qim3d/ml/_ml_utils.py
@@ -4,8 +4,8 @@ import torch
import numpy as np
from torchinfo import summary
-from qim3d.utils.logger import log
-from qim3d.viz.metrics import plot_metrics
+from qim3d.utils._logger import log
+from qim3d.viz._metrics import plot_metrics
from tqdm.auto import tqdm
from tqdm.contrib.logging import logging_redirect_tqdm
diff --git a/qim3d/ml/models/__init__.py b/qim3d/ml/models/__init__.py
new file mode 100644
index 00000000..4624be5f
--- /dev/null
+++ b/qim3d/ml/models/__init__.py
@@ -0,0 +1 @@
+from ._unet import UNet, Hyperparameters
diff --git a/qim3d/models/unet.py b/qim3d/ml/models/_unet.py
similarity index 99%
rename from qim3d/models/unet.py
rename to qim3d/ml/models/_unet.py
index 6c57f55e..353d10bd 100644
--- a/qim3d/models/unet.py
+++ b/qim3d/ml/models/_unet.py
@@ -2,7 +2,7 @@
import torch.nn as nn
-from qim3d.utils.logger import log
+from qim3d.utils._logger import log
class UNet(nn.Module):
diff --git a/qim3d/models/__init__.py b/qim3d/models/__init__.py
deleted file mode 100644
index a145a44f..00000000
--- a/qim3d/models/__init__.py
+++ /dev/null
@@ -1,4 +0,0 @@
-from .unet import UNet, Hyperparameters
-from .augmentations import Augmentation
-from .data import Dataset, prepare_dataloaders, prepare_datasets
-from .models import inference, model_summary, train_model
diff --git a/qim3d/operations/__init__.py b/qim3d/operations/__init__.py
new file mode 100644
index 00000000..add2a011
--- /dev/null
+++ b/qim3d/operations/__init__.py
@@ -0,0 +1 @@
+from ._common_operations_methods import *
diff --git a/qim3d/processing/operations.py b/qim3d/operations/_common_operations_methods.py
similarity index 76%
rename from qim3d/processing/operations.py
rename to qim3d/operations/_common_operations_methods.py
index e559a16d..1c14e163 100644
--- a/qim3d/processing/operations.py
+++ b/qim3d/operations/_common_operations_methods.py
@@ -1,7 +1,8 @@
import numpy as np
-import qim3d.processing.filters as filters
-from qim3d.utils.logger import log
+import qim3d.filters as filters
+from qim3d.utils._logger import log
+__all__ = ["remove_background", "fade_mask", "overlay_rgb_images"]
def remove_background(
vol: np.ndarray,
@@ -29,7 +30,7 @@ def remove_background(
import qim3d
vol = qim3d.examples.cement_128x128x128
- qim3d.viz.slices(vol, vmin=0, vmax=255)
+ qim3d.viz.slices_grid(vol, vmin=0, vmax=255)
```
@@ -37,7 +38,7 @@ def remove_background(
vol_filtered = qim3d.processing.operations.remove_background(vol,
min_object_radius=3,
background="bright")
- qim3d.viz.slices(vol_filtered, vmin=0, vmax=255)
+ qim3d.viz.slices_grid(vol_filtered, vmin=0, vmax=255)
```
"""
@@ -52,74 +53,6 @@ def remove_background(
return pipeline(vol)
-def watershed(bin_vol: np.ndarray, min_distance: int = 5) -> tuple[np.ndarray, int]:
- """
- Apply watershed segmentation to a binary volume.
-
- Args:
- bin_vol (np.ndarray): Binary volume to segment. The input should be a 3D binary image where non-zero elements
- represent the objects to be segmented.
- min_distance (int): Minimum number of pixels separating peaks in the distance transform. Peaks that are
- too close will be merged, affecting the number of segmented objects. Default is 5.
-
- Returns:
- tuple[np.ndarray, int]:
- - Labeled volume (np.ndarray): A 3D array of the same shape as the input `bin_vol`, where each segmented object
- is assigned a unique integer label.
- - num_labels (int): The total number of unique objects found in the labeled volume.
-
- Example:
- ```python
- import qim3d
-
- vol = qim3d.examples.cement_128x128x128
- binary = qim3d.processing.filters.gaussian(vol, sigma = 2)<60
-
- qim3d.viz.slices(binary, axis=1)
- ```
- 
-
- ```python
- labeled_volume, num_labels = qim3d.processing.operations.watershed(binary)
-
- cmap = qim3d.viz.colormaps.objects(num_labels)
- qim3d.viz.slices(labeled_volume, axis = 1, cmap = cmap)
- ```
- 
-
- """
- import skimage
- import scipy
-
- if len(np.unique(bin_vol)) > 2:
- raise ValueError("bin_vol has to be binary volume - it must contain max 2 unique values.")
-
- # Compute distance transform of binary volume
- distance = scipy.ndimage.distance_transform_edt(bin_vol)
-
- # Find peak coordinates in distance transform
- coords = skimage.feature.peak_local_max(
- distance, min_distance=min_distance, labels=bin_vol
- )
-
- # Create a mask with peak coordinates
- mask = np.zeros(distance.shape, dtype=bool)
- mask[tuple(coords.T)] = True
-
- # Label peaks
- markers, _ = scipy.ndimage.label(mask)
-
- # Apply watershed segmentation
- labeled_volume = skimage.segmentation.watershed(
- -distance, markers=markers, mask=bin_vol
- )
-
- # Extract number of objects found
- num_labels = len(np.unique(labeled_volume)) - 1
- log.info(f"Total number of objects found: {num_labels}")
-
- return labeled_volume, num_labels
-
def fade_mask(
vol: np.ndarray,
diff --git a/qim3d/processing/__init__.py b/qim3d/processing/__init__.py
index 8f6edf04..913d6ddb 100644
--- a/qim3d/processing/__init__.py
+++ b/qim3d/processing/__init__.py
@@ -1,9 +1,3 @@
-from .local_thickness_ import local_thickness
-from .structure_tensor_ import structure_tensor
-from .detection import blob_detection
-from .filters import *
-from .operations import *
-from .cc import get_3d_cc
-from .layers2d import segment_layers, get_lines
-from .mesh import create_mesh
-from .features import volume, area, sphericity
+from ._local_thickness import local_thickness
+from ._structure_tensor import structure_tensor
+from ._layers import segment_layers, get_lines
diff --git a/qim3d/processing/layers2d.py b/qim3d/processing/_layers.py
similarity index 100%
rename from qim3d/processing/layers2d.py
rename to qim3d/processing/_layers.py
diff --git a/qim3d/processing/local_thickness_.py b/qim3d/processing/_local_thickness.py
similarity index 99%
rename from qim3d/processing/local_thickness_.py
rename to qim3d/processing/_local_thickness.py
index f106cbcb..a7e877d6 100644
--- a/qim3d/processing/local_thickness_.py
+++ b/qim3d/processing/_local_thickness.py
@@ -2,7 +2,7 @@
import numpy as np
from typing import Optional
-from qim3d.utils.logger import log
+from qim3d.utils._logger import log
import qim3d
diff --git a/qim3d/processing/structure_tensor_.py b/qim3d/processing/_structure_tensor.py
similarity index 98%
rename from qim3d/processing/structure_tensor_.py
rename to qim3d/processing/_structure_tensor.py
index 97a0ba73..10eba890 100644
--- a/qim3d/processing/structure_tensor_.py
+++ b/qim3d/processing/_structure_tensor.py
@@ -3,7 +3,7 @@
from typing import Tuple
import logging
import numpy as np
-from qim3d.utils.logger import log
+from qim3d.utils._logger import log
def structure_tensor(
@@ -108,7 +108,7 @@ def structure_tensor(
val, vec = st.eig_special_3d(s_vol, full=full)
if visualize:
- from qim3d.viz.structure_tensor import vectors
+ from qim3d.viz._structure_tensor import vectors
display(vectors(vol, vec, **viz_kwargs))
diff --git a/qim3d/segmentation/__init__.py b/qim3d/segmentation/__init__.py
new file mode 100644
index 00000000..efdd6232
--- /dev/null
+++ b/qim3d/segmentation/__init__.py
@@ -0,0 +1,2 @@
+from ._common_segmentation_methods import *
+from ._connected_components import get_3d_cc
diff --git a/qim3d/segmentation/_common_segmentation_methods.py b/qim3d/segmentation/_common_segmentation_methods.py
new file mode 100644
index 00000000..ba4f231d
--- /dev/null
+++ b/qim3d/segmentation/_common_segmentation_methods.py
@@ -0,0 +1,72 @@
+import numpy as np
+from qim3d.utils._logger import log
+
+__all__ = ["watershed"]
+
+def watershed(bin_vol: np.ndarray, min_distance: int = 5) -> tuple[np.ndarray, int]:
+ """
+ Apply watershed segmentation to a binary volume.
+
+ Args:
+ bin_vol (np.ndarray): Binary volume to segment. The input should be a 3D binary image where non-zero elements
+ represent the objects to be segmented.
+ min_distance (int): Minimum number of pixels separating peaks in the distance transform. Peaks that are
+ too close will be merged, affecting the number of segmented objects. Default is 5.
+
+ Returns:
+ tuple[np.ndarray, int]:
+ - Labeled volume (np.ndarray): A 3D array of the same shape as the input `bin_vol`, where each segmented object
+ is assigned a unique integer label.
+ - num_labels (int): The total number of unique objects found in the labeled volume.
+
+ Example:
+ ```python
+ import qim3d
+
+ vol = qim3d.examples.cement_128x128x128
+ binary = qim3d.processing.filters.gaussian(vol, sigma = 2)<60
+
+ qim3d.viz.slices_grid(binary, axis=1)
+ ```
+ 
+
+ ```python
+ labeled_volume, num_labels = qim3d.processing.operations.watershed(binary)
+
+ cmap = qim3d.viz.colormaps.objects(num_labels)
+ qim3d.viz.slices_grid(labeled_volume, axis = 1, cmap = cmap)
+ ```
+ 
+
+ """
+ import skimage
+ import scipy
+
+ if len(np.unique(bin_vol)) > 2:
+ raise ValueError("bin_vol has to be binary volume - it must contain max 2 unique values.")
+
+ # Compute distance transform of binary volume
+ distance = scipy.ndimage.distance_transform_edt(bin_vol)
+
+ # Find peak coordinates in distance transform
+ coords = skimage.feature.peak_local_max(
+ distance, min_distance=min_distance, labels=bin_vol
+ )
+
+ # Create a mask with peak coordinates
+ mask = np.zeros(distance.shape, dtype=bool)
+ mask[tuple(coords.T)] = True
+
+ # Label peaks
+ markers, _ = scipy.ndimage.label(mask)
+
+ # Apply watershed segmentation
+ labeled_volume = skimage.segmentation.watershed(
+ -distance, markers=markers, mask=bin_vol
+ )
+
+ # Extract number of objects found
+ num_labels = len(np.unique(labeled_volume)) - 1
+ log.info(f"Total number of objects found: {num_labels}")
+
+ return labeled_volume, num_labels
\ No newline at end of file
diff --git a/qim3d/processing/cc.py b/qim3d/segmentation/_connected_components.py
similarity index 98%
rename from qim3d/processing/cc.py
rename to qim3d/segmentation/_connected_components.py
index 43283c23..f43f0dc2 100644
--- a/qim3d/processing/cc.py
+++ b/qim3d/segmentation/_connected_components.py
@@ -1,6 +1,6 @@
import numpy as np
from scipy.ndimage import find_objects, label
-from qim3d.utils.logger import log
+from qim3d.utils._logger import log
class CC:
diff --git a/qim3d/tests/__init__.py b/qim3d/tests/__init__.py
index c08e68dd..1fa15c27 100644
--- a/qim3d/tests/__init__.py
+++ b/qim3d/tests/__init__.py
@@ -8,7 +8,7 @@ import shutil
from PIL import Image
import socket
import numpy as np
-from qim3d.utils.logger import log
+from qim3d.utils._logger import log
def mock_plot():
diff --git a/qim3d/tests/processing/test_connected_components.py b/qim3d/tests/processing/test_connected_components.py
index 0e972123..9d59aff9 100644
--- a/qim3d/tests/processing/test_connected_components.py
+++ b/qim3d/tests/processing/test_connected_components.py
@@ -1,7 +1,7 @@
import numpy as np
import pytest
-from qim3d.processing.cc import get_3d_cc
+from qim3d.segmentation._connected_components import get_3d_cc
@pytest.fixture(scope="module")
diff --git a/qim3d/tests/processing/test_filters.py b/qim3d/tests/processing/test_filters.py
index e6362811..5a6d0993 100644
--- a/qim3d/tests/processing/test_filters.py
+++ b/qim3d/tests/processing/test_filters.py
@@ -1,5 +1,5 @@
import qim3d
-from qim3d.processing.filters import *
+from qim3d.filters import *
import numpy as np
import pytest
import re
diff --git a/qim3d/tests/viz/test_img.py b/qim3d/tests/viz/test_img.py
index bcbed39d..ec959910 100644
--- a/qim3d/tests/viz/test_img.py
+++ b/qim3d/tests/viz/test_img.py
@@ -52,14 +52,14 @@ def test_grid_pred():
# unit tests for slices function
def test_slices_numpy_array_input():
example_volume = np.ones((10, 10, 10))
- fig = qim3d.viz.slices(example_volume, n_slices=1)
+ fig = qim3d.viz.slices_grid(example_volume, n_slices=1)
assert isinstance(fig, plt.Figure)
def test_slices_wrong_input_format():
input = "not_a_volume"
with pytest.raises(ValueError, match="Data type not supported"):
- qim3d.viz.slices(input)
+ qim3d.viz.slices_grid(input)
def test_slices_not_volume():
@@ -68,7 +68,7 @@ def test_slices_not_volume():
ValueError,
match="The provided object is not a volume as it has less than 3 dimensions.",
):
- qim3d.viz.slices(example_volume)
+ qim3d.viz.slices_grid(example_volume)
def test_slices_wrong_position_format1():
@@ -77,7 +77,7 @@ def test_slices_wrong_position_format1():
ValueError,
match='Position not recognized. Choose an integer, list of integers or one of the following strings: "start", "mid" or "end".',
):
- qim3d.viz.slices(example_volume, position="invalid_slice")
+ qim3d.viz.slices_grid(example_volume, position="invalid_slice")
def test_slices_wrong_position_format2():
@@ -86,7 +86,7 @@ def test_slices_wrong_position_format2():
ValueError,
match='Position not recognized. Choose an integer, list of integers or one of the following strings: "start", "mid" or "end".',
):
- qim3d.viz.slices(example_volume, position=1.5)
+ qim3d.viz.slices_grid(example_volume, position=1.5)
def test_slices_wrong_position_format3():
@@ -95,7 +95,7 @@ def test_slices_wrong_position_format3():
ValueError,
match='Position not recognized. Choose an integer, list of integers or one of the following strings: "start", "mid" or "end".',
):
- qim3d.viz.slices(example_volume, position=[1, 2, 3.5])
+ qim3d.viz.slices_grid(example_volume, position=[1, 2, 3.5])
def test_slices_invalid_axis_value():
@@ -104,14 +104,14 @@ def test_slices_invalid_axis_value():
ValueError,
match="Invalid value for 'axis'. It should be an integer between 0 and 2",
):
- qim3d.viz.slices(example_volume, axis=3)
+ qim3d.viz.slices_grid(example_volume, axis=3)
def test_slices_interpolation_option():
example_volume = np.ones((10, 10, 10))
img_width = 3
interpolation_method = "bilinear"
- fig = qim3d.viz.slices(
+ fig = qim3d.viz.slices_grid(
example_volume,
n_slices=1,
img_width=img_width,
@@ -130,7 +130,7 @@ def test_slices_multiple_slices():
example_volume = np.ones((10, 10, 10))
img_width = 3
n_slices = 3
- fig = qim3d.viz.slices(example_volume, n_slices=n_slices, img_width=img_width)
+ fig = qim3d.viz.slices_grid(example_volume, n_slices=n_slices, img_width=img_width)
# Add assertions for the expected number of subplots in the figure
assert len(fig.get_axes()) == n_slices
@@ -141,13 +141,13 @@ def test_slices_axis_argument():
img_width = 3
# Call the function with different values of the axis
- fig_axis_0 = qim3d.viz.slices(
+ fig_axis_0 = qim3d.viz.slices_grid(
example_volume, n_slices=1, img_width=img_width, axis=0
)
- fig_axis_1 = qim3d.viz.slices(
+ fig_axis_1 = qim3d.viz.slices_grid(
example_volume, n_slices=1, img_width=img_width, axis=1
)
- fig_axis_2 = qim3d.viz.slices(
+ fig_axis_2 = qim3d.viz.slices_grid(
example_volume, n_slices=1, img_width=img_width, axis=2
)
diff --git a/qim3d/utils/__init__.py b/qim3d/utils/__init__.py
index e9eb7e7f..0c7d5b30 100644
--- a/qim3d/utils/__init__.py
+++ b/qim3d/utils/__init__.py
@@ -1,7 +1,7 @@
-from . import doi
-from .system import Memory
+from . import _doi
+from ._system import Memory
-from .misc import (
+from ._misc import (
get_local_ip,
port_from_str,
gradio_header,
@@ -13,4 +13,4 @@ from .misc import (
scale_to_float16,
)
-from .server import start_http_server
\ No newline at end of file
+from ._server import start_http_server
\ No newline at end of file
diff --git a/qim3d/utils/cli.py b/qim3d/utils/_cli.py
similarity index 100%
rename from qim3d/utils/cli.py
rename to qim3d/utils/_cli.py
diff --git a/qim3d/utils/doi.py b/qim3d/utils/_doi.py
similarity index 98%
rename from qim3d/utils/doi.py
rename to qim3d/utils/_doi.py
index 60e01d76..b3ece663 100644
--- a/qim3d/utils/doi.py
+++ b/qim3d/utils/_doi.py
@@ -1,7 +1,7 @@
""" Deals with DOI for references """
import json
import requests
-from qim3d.utils.logger import log
+from qim3d.utils._logger import log
def _validate_response(response):
diff --git a/qim3d/utils/logger.py b/qim3d/utils/_logger.py
similarity index 100%
rename from qim3d/utils/logger.py
rename to qim3d/utils/_logger.py
diff --git a/qim3d/utils/misc.py b/qim3d/utils/_misc.py
similarity index 100%
rename from qim3d/utils/misc.py
rename to qim3d/utils/_misc.py
diff --git a/qim3d/utils/ome_zarr.py b/qim3d/utils/_ome_zarr.py
similarity index 100%
rename from qim3d/utils/ome_zarr.py
rename to qim3d/utils/_ome_zarr.py
diff --git a/qim3d/utils/progress_bar.py b/qim3d/utils/_progress_bar.py
similarity index 99%
rename from qim3d/utils/progress_bar.py
rename to qim3d/utils/_progress_bar.py
index 6790b1bf..629026f4 100644
--- a/qim3d/utils/progress_bar.py
+++ b/qim3d/utils/_progress_bar.py
@@ -6,7 +6,7 @@ from abc import ABC, abstractmethod
from tqdm.auto import tqdm
-from qim3d.utils.misc import get_file_size
+from qim3d.utils._misc import get_file_size
class RepeatTimer(Timer):
diff --git a/qim3d/utils/server.py b/qim3d/utils/_server.py
similarity index 98%
rename from qim3d/utils/server.py
rename to qim3d/utils/_server.py
index 65344f1b..9d20fccd 100644
--- a/qim3d/utils/server.py
+++ b/qim3d/utils/_server.py
@@ -1,7 +1,7 @@
import os
from http.server import SimpleHTTPRequestHandler, HTTPServer
import threading
-from qim3d.utils.logger import log
+from qim3d.utils._logger import log
class CustomHTTPRequestHandler(SimpleHTTPRequestHandler):
def end_headers(self):
diff --git a/qim3d/utils/system.py b/qim3d/utils/_system.py
similarity index 98%
rename from qim3d/utils/system.py
rename to qim3d/utils/_system.py
index 39dc3af7..19792627 100644
--- a/qim3d/utils/system.py
+++ b/qim3d/utils/_system.py
@@ -2,8 +2,8 @@
import os
import time
import psutil
-from qim3d.utils.misc import sizeof
-from qim3d.utils.logger import log
+from qim3d.utils._misc import sizeof
+from qim3d.utils._logger import log
import numpy as np
diff --git a/qim3d/viz/__init__.py b/qim3d/viz/__init__.py
index 33d94416..bc65ee16 100644
--- a/qim3d/viz/__init__.py
+++ b/qim3d/viz/__init__.py
@@ -1,18 +1,18 @@
from . import colormaps
-from .cc import plot_cc
-from .detection import circles
-from .explore import (
- interactive_fade_mask,
- orthogonal,
+from ._cc import plot_cc
+from ._detection import circles
+from ._data_exploration import (
+ fade_mask,
slicer,
- slices,
+ slicer_orthogonal,
+ slices_grid,
chunks,
histogram,
)
from .itk_vtk_viewer import itk_vtk, Installer, NotInstalledError
-from .k3d import vol, mesh
-from .local_thickness_ import local_thickness
-from .structure_tensor import vectors
-from .metrics import plot_metrics, grid_overview, grid_pred, vol_masked
-from .preview import image_preview
-from . import layers2d
+from ._k3d import volumetric, mesh
+from ._local_thickness import local_thickness
+from ._structure_tensor import vectors
+from ._metrics import plot_metrics, grid_overview, grid_pred, vol_masked
+from ._preview import image_preview
+from . import _layers2d
diff --git a/qim3d/viz/cc.py b/qim3d/viz/_cc.py
similarity index 90%
rename from qim3d/viz/cc.py
rename to qim3d/viz/_cc.py
index b7dd999e..1c0ed560 100644
--- a/qim3d/viz/cc.py
+++ b/qim3d/viz/_cc.py
@@ -1,8 +1,7 @@
import matplotlib.pyplot as plt
import numpy as np
-
-from qim3d.utils.logger import log
-import qim3d.viz.colormaps
+import qim3d
+from qim3d.utils._logger import log
def plot_cc(
@@ -12,9 +11,9 @@ def plot_cc(
overlay=None,
crop=False,
show=True,
- cmap:str = 'viridis',
- vmin:float = None,
- vmax:float = None,
+ cmap: str = "viridis",
+ vmin: float = None,
+ vmax: float = None,
**kwargs,
) -> list[plt.Figure]:
"""
@@ -30,7 +29,7 @@ def plot_cc(
cmap (str, optional): Specifies the color map for the image. Defaults to "viridis".
vmin (float, optional): Together with vmax define the data range the colormap covers. By default colormap covers the full range. Defaults to None.
vmax (float, optional): Together with vmin define the data range the colormap covers. By default colormap covers the full range. Defaults to None
- **kwargs: Additional keyword arguments to pass to `qim3d.viz.slices`.
+ **kwargs: Additional keyword arguments to pass to `qim3d.viz.slices_grid`.
Returns:
figs (list[plt.Figure]): List of figures, if `show=False`.
@@ -75,14 +74,16 @@ def plot_cc(
else:
cc = connected_components.get_cc(component, crop=False)
overlay_crop = np.where(cc == 0, 0, overlay)
- fig = qim3d.viz.slices(overlay_crop, show=show, cmap = cmap, vmin = vmin, vmax = vmax, **kwargs)
+ fig = qim3d.viz.slices_grid(
+ overlay_crop, show=show, cmap=cmap, vmin=vmin, vmax=vmax, **kwargs
+ )
else:
# assigns discrete color map to each connected component if not given
if "cmap" not in kwargs:
- kwargs["cmap"] = qim3d.viz.colormaps.objects(len(component_indexs))
+ kwargs["cmap"] = qim3d.viz.colormaps.segmentation(len(component_indexs))
# Plot the connected component without overlay
- fig = qim3d.viz.slices(
+ fig = qim3d.viz.slices_grid(
connected_components.get_cc(component, crop=crop), show=show, **kwargs
)
diff --git a/qim3d/viz/explore.py b/qim3d/viz/_data_exploration.py
similarity index 61%
rename from qim3d/viz/explore.py
rename to qim3d/viz/_data_exploration.py
index 8fe2a545..2198cd94 100644
--- a/qim3d/viz/explore.py
+++ b/qim3d/viz/_data_exploration.py
@@ -14,150 +14,162 @@ from IPython.display import SVG, display
import matplotlib
import numpy as np
import zarr
-from qim3d.utils.logger import log
+from qim3d.utils._logger import log
import seaborn as sns
import qim3d
-def slices(
- vol: np.ndarray,
- axis: int = 0,
- position: Optional[Union[str, int, List[int]]] = None,
- n_slices: int = 5,
- max_cols: int = 5,
- cmap: str = "viridis",
- vmin: float = None,
- vmax: float = None,
- img_height: int = 2,
- img_width: int = 2,
- show: bool = False,
- show_position: bool = True,
+
+def slices_grid(
+ volume: np.ndarray,
+ slice_axis: int = 0,
+ slice_positions: Optional[Union[str, int, List[int]]] = None,
+ num_slices: int = 15,
+ max_columns: int = 5,
+ color_map: str = "magma",
+ value_min: float = None,
+ value_max: float = None,
+ image_size=None,
+ image_height: int = 2,
+ image_width: int = 2,
+ display_figure: bool = False,
+ display_positions: bool = True,
interpolation: Optional[str] = None,
- img_size=None,
- cbar: bool = False,
- cbar_style: str = "small",
- **imshow_kwargs,
+ color_bar: bool = False,
+ color_bar_style: str = "small",
+ **matplotlib_imshow_kwargs,
) -> plt.Figure:
"""Displays one or several slices from a 3d volume.
- By default if `position` is None, slices plots `n_slices` linearly spaced slices.
- If `position` is given as a string or integer, slices will plot an overview with `n_slices` figures around that position.
- If `position` is given as a list, `n_slices` will be ignored and the slices from `position` will be plotted.
+ By default if `slice_positions` is None, slices_grid plots `num_slices` linearly spaced slices.
+ If `slice_positions` is given as a string or integer, slices_grid will plot an overview with `num_slices` figures around that position.
+ If `slice_positions` is given as a list, `num_slices` will be ignored and the slices from `slice_positions` will be plotted.
Args:
vol np.ndarray: The 3D volume to be sliced.
- axis (int, optional): Specifies the axis, or dimension, along which to slice. Defaults to 0.
- position (str, int, list, optional): One or several slicing levels. If None, linearly spaced slices will be displayed. Defaults to None.
- n_slices (int, optional): Defines how many slices the user wants to be displayed. Defaults to 5.
- max_cols (int, optional): The maximum number of columns to be plotted. Defaults to 5.
- cmap (str, optional): Specifies the color map for the image. Defaults to "viridis".
- vmin (float, optional): Together with vmax define the data range the colormap covers. By default colormap covers the full range. Defaults to None.
- vmax (float, optional): Together with vmin define the data range the colormap covers. By default colormap covers the full range. Defaults to None
- img_height (int, optional): Height of the figure.
- img_width (int, optional): Width of the figure.
- show (bool, optional): If True, displays the plot (i.e. calls plt.show()). Defaults to False.
- show_position (bool, optional): If True, displays the position of the slices. Defaults to True.
+ slice_axis (int, optional): Specifies the axis, or dimension, along which to slice. Defaults to 0.
+ slice_positions (str, int, list, optional): One or several slicing levels. If None, linearly spaced slices will be displayed. Defaults to None.
+ num_slices (int, optional): Defines how many slices the user wants to be displayed. Defaults to 15.
+ max_columns (int, optional): The maximum number of columns to be plotted. Defaults to 5.
+ color_map (str, optional): Specifies the color map for the image. Defaults to "viridis".
+ value_min (float, optional): Together with value_max define the data range the colormap covers. By default colormap covers the full range. Defaults to None.
+ value_max (float, optional): Together with value_min define the data range the colormap covers. By default colormap covers the full range. Defaults to None
+ image_height (int, optional): Height of the figure.
+ image_width (int, optional): Width of the figure.
+ display_figure (bool, optional): If True, displays the plot (i.e. calls plt.show()). Defaults to False.
+ display_positions (bool, optional): If True, displays the position of the slices. Defaults to True.
interpolation (str, optional): Specifies the interpolation method for the image. Defaults to None.
- cbar (bool, optional): Adds a colorbar positioned in the top-right for the corresponding colormap and data range. Defaults to False.
- cbar_style (str, optional): Determines the style of the colorbar. Option 'small' is height of one image row. Option 'large' spans full height of image grid. Defaults to 'small'.
+ color_bar (bool, optional): Adds a colorbar positioned in the top-right for the corresponding colormap and data range. Defaults to False.
+ color_bar_style (str, optional): Determines the style of the colorbar. Option 'small' is height of one image row. Option 'large' spans full height of image grid. Defaults to 'small'.
Returns:
fig (matplotlib.figure.Figure): The figure with the slices from the 3d array.
Raises:
ValueError: If the input is not a numpy.ndarray or da.core.Array.
- ValueError: If the axis to slice along is not a valid choice, i.e. not an integer between 0 and the number of dimensions of the volume minus 1.
+ ValueError: If the slice_axis to slice along is not a valid choice, i.e. not an integer between 0 and the number of dimensions of the volume minus 1.
ValueError: If the file or array is not a volume with at least 3 dimensions.
ValueError: If the `position` keyword argument is not a integer, list of integers or one of the following strings: "start", "mid" or "end".
- ValueError: If the cbar_style keyword argument is not one of the following strings: 'small' or 'large'.
+ ValueError: If the color_bar_style keyword argument is not one of the following strings: 'small' or 'large'.
Example:
```python
import qim3d
vol = qim3d.examples.shell_225x128x128
- qim3d.viz.slices(vol, n_slices=15)
+ qim3d.viz.slices_grid_grid(vol, num_slices=15)
```
"""
- if img_size:
- img_height = img_size
- img_width = img_size
+ if image_size:
+ image_height = image_size
+ image_width = image_size
- # If we pass python None to the imshow function, it will set to
+ # If we pass python None to the imshow function, it will set to
# default value 'antialiased'
if interpolation is None:
- interpolation = 'none'
+ interpolation = "none"
# Numpy array or Torch tensor input
- if not isinstance(vol, (np.ndarray, da.core.Array)):
+ if not isinstance(volume, (np.ndarray, da.core.Array)):
raise ValueError("Data type not supported")
- if vol.ndim < 3:
+ if volume.ndim < 3:
raise ValueError(
"The provided object is not a volume as it has less than 3 dimensions."
)
- cbar_style_options = ["small", "large"]
- if cbar_style not in cbar_style_options:
- raise ValueError(f"Value '{cbar_style}' is not valid for colorbar style. Please select from {cbar_style_options}.")
-
- if isinstance(vol, da.core.Array):
- vol = vol.compute()
+ color_bar_style_options = ["small", "large"]
+ if color_bar_style not in color_bar_style_options:
+ raise ValueError(
+ f"Value '{color_bar_style}' is not valid for colorbar style. Please select from {color_bar_style_options}."
+ )
+
+ if isinstance(volume, da.core.Array):
+ volume = volume.compute()
# Ensure axis is a valid choice
- if not (0 <= axis < vol.ndim):
+ if not (0 <= slice_axis < volume.ndim):
raise ValueError(
- f"Invalid value for 'axis'. It should be an integer between 0 and {vol.ndim - 1}."
+ f"Invalid value for 'slice_axis'. It should be an integer between 0 and {volume.ndim - 1}."
)
- if type(cmap) == matplotlib.colors.LinearSegmentedColormap or cmap == 'objects':
- num_labels = len(np.unique(vol))
+ # Here we deal with the case that the user wants to use the objects colormap directly
+ if (
+ type(color_map) == matplotlib.colors.LinearSegmentedColormap
+ or color_map == "segmentation"
+ ):
+ num_labels = len(np.unique(volume))
- if cmap == 'objects':
- cmap = qim3d.viz.colormaps.objects(num_labels)
- # If vmin and vmax are not set like this, then in case the
- # number of objects changes on new slice, objects might change
- # colors. So when using a slider, the same object suddently
+ if color_map == "segmentation":
+ color_map = qim3d.viz.colormaps.segmentation(num_labels)
+ # If value_min and value_max are not set like this, then in case the
+ # number of objects changes on new slice, objects might change
+ # colors. So when using a slider, the same object suddently
# changes color (flickers), which is confusing and annoying.
- vmin = 0
- vmax = num_labels
-
+ value_min = 0
+ value_max = num_labels
# Get total number of slices in the specified dimension
- n_total = vol.shape[axis]
+ n_total = volume.shape[slice_axis]
# Position is not provided - will use linearly spaced slices
- if position is None:
- slice_idxs = np.linspace(0, n_total - 1, n_slices, dtype=int)
+ if slice_positions is None:
+ slice_idxs = np.linspace(0, n_total - 1, num_slices, dtype=int)
# Position is a string
- elif isinstance(position, str) and position.lower() in ["start", "mid", "end"]:
- if position.lower() == "start":
- slice_idxs = _get_slice_range(0, n_slices, n_total)
- elif position.lower() == "mid":
- slice_idxs = _get_slice_range(n_total // 2, n_slices, n_total)
- elif position.lower() == "end":
- slice_idxs = _get_slice_range(n_total - 1, n_slices, n_total)
+ elif isinstance(slice_positions, str) and slice_positions.lower() in [
+ "start",
+ "mid",
+ "end",
+ ]:
+ if slice_positions.lower() == "start":
+ slice_idxs = _get_slice_range(0, num_slices, n_total)
+ elif slice_positions.lower() == "mid":
+ slice_idxs = _get_slice_range(n_total // 2, num_slices, n_total)
+ elif slice_positions.lower() == "end":
+ slice_idxs = _get_slice_range(n_total - 1, num_slices, n_total)
# Position is an integer
- elif isinstance(position, int):
- slice_idxs = _get_slice_range(position, n_slices, n_total)
+ elif isinstance(slice_positions, int):
+ slice_idxs = _get_slice_range(slice_positions, num_slices, n_total)
# Position is a list of integers
- elif isinstance(position, list) and all(isinstance(idx, int) for idx in position):
- slice_idxs = position
+ elif isinstance(slice_positions, list) and all(
+ isinstance(idx, int) for idx in slice_positions
+ ):
+ slice_idxs = slice_positions
else:
raise ValueError(
'Position not recognized. Choose an integer, list of integers or one of the following strings: "start", "mid" or "end".'
)
# Make grid
- nrows = math.ceil(n_slices / max_cols)
- ncols = min(n_slices, max_cols)
+ nrows = math.ceil(num_slices / max_columns)
+ ncols = min(num_slices, max_columns)
# Generate figure
fig, axs = plt.subplots(
nrows=nrows,
ncols=ncols,
- figsize=(ncols * img_height, nrows * img_width),
+ figsize=(ncols * image_height, nrows * image_width),
constrained_layout=True,
)
@@ -165,47 +177,53 @@ def slices(
axs = [axs] # Convert to a list for uniformity
# Convert to NumPy array in order to use the numpy.take method
- if isinstance(vol, da.core.Array):
- vol = vol.compute()
+ if isinstance(volume, da.core.Array):
+ volume = volume.compute()
- if cbar:
- # In this case, we want the vrange to be constant across the
- # slices, which makes them all comparable to a single cbar.
- new_vmin = vmin if vmin is not None else np.min(vol)
- new_vmax = vmax if vmax is not None else np.max(vol)
+ if color_bar:
+ # In this case, we want the vrange to be constant across the
+ # slices, which makes them all comparable to a single color_bar.
+ new_value_min = value_min if value_min is not None else np.min(volume)
+ new_value_max = value_max if value_max is not None else np.max(volume)
# Run through each ax of the grid
for i, ax_row in enumerate(axs):
for j, ax in enumerate(np.atleast_1d(ax_row)):
- slice_idx = i * max_cols + j
+ slice_idx = i * max_columns + j
try:
- slice_img = vol.take(slice_idxs[slice_idx], axis=axis)
+ slice_img = volume.take(slice_idxs[slice_idx], axis=slice_axis)
- if not cbar:
- # If vmin is higher than the highest value in the
- # image ValueError is raised. We don't want to
+ if not color_bar:
+ # If value_min is higher than the highest value in the
+ # image ValueError is raised. We don't want to
# override the values because next slices might be okay
- new_vmin = (
+ new_value_min = (
None
- if (isinstance(vmin, (float, int)) and vmin > np.max(slice_img))
- else vmin
+ if (
+ isinstance(value_min, (float, int))
+ and value_min > np.max(slice_img)
+ )
+ else value_min
)
- new_vmax = (
+ new_value_max = (
None
- if (isinstance(vmax, (float, int)) and vmax < np.min(slice_img))
- else vmax
+ if (
+ isinstance(value_max, (float, int))
+ and value_max < np.min(slice_img)
+ )
+ else value_max
)
ax.imshow(
slice_img,
- cmap=cmap,
+ cmap=color_map,
interpolation=interpolation,
- vmin=new_vmin,
- vmax=new_vmax,
- **imshow_kwargs,
+ vmin=new_value_min,
+ vmax=new_value_max,
+ **matplotlib_imshow_kwargs,
)
- if show_position:
+ if display_positions:
ax.text(
0.0,
1.0,
@@ -221,7 +239,7 @@ def slices(
ax.text(
1.0,
0.0,
- f"axis {axis} ",
+ f"axis {slice_axis} ",
transform=ax.transAxes,
color="white",
fontsize=8,
@@ -237,33 +255,40 @@ def slices(
# Hide the axis, so that we have a nice grid
ax.axis("off")
- if cbar:
+ if color_bar:
with warnings.catch_warnings():
warnings.simplefilter("ignore", category=UserWarning)
fig.tight_layout()
- norm = matplotlib.colors.Normalize(vmin=new_vmin, vmax=new_vmax, clip=True)
- mappable = matplotlib.cm.ScalarMappable(norm=norm, cmap=cmap)
+ norm = matplotlib.colors.Normalize(
+ vmin=new_value_min, vmax=new_value_max, clip=True
+ )
+ mappable = matplotlib.cm.ScalarMappable(norm=norm, cmap=color_map)
- if cbar_style =="small":
+ if color_bar_style == "small":
# Figure coordinates of top-right axis
tr_pos = np.atleast_1d(axs[0])[-1].get_position()
# The width is divided by ncols to make it the same relative size to the images
- cbar_ax = fig.add_axes(
+ color_bar_ax = fig.add_axes(
[tr_pos.x1 + 0.05 / ncols, tr_pos.y0, 0.05 / ncols, tr_pos.height]
)
- fig.colorbar(mappable=mappable, cax=cbar_ax, orientation="vertical")
- elif cbar_style == "large":
+ fig.colorbar(mappable=mappable, cax=color_bar_ax, orientation="vertical")
+ elif color_bar_style == "large":
# Figure coordinates of bottom- and top-right axis
br_pos = np.atleast_1d(axs[-1])[-1].get_position()
tr_pos = np.atleast_1d(axs[0])[-1].get_position()
# The width is divided by ncols to make it the same relative size to the images
- cbar_ax = fig.add_axes(
- [br_pos.xmax + 0.05 / ncols, br_pos.y0+0.0015, 0.05 / ncols, (tr_pos.y1 - br_pos.y0)-0.0015]
+ color_bar_ax = fig.add_axes(
+ [
+ br_pos.xmax + 0.05 / ncols,
+ br_pos.y0 + 0.0015,
+ 0.05 / ncols,
+ (tr_pos.y1 - br_pos.y0) - 0.0015,
+ ]
)
- fig.colorbar(mappable=mappable, cax=cbar_ax, orientation="vertical")
+ fig.colorbar(mappable=mappable, cax=color_bar_ax, orientation="vertical")
- if show:
+ if display_figure:
plt.show()
plt.close()
@@ -271,49 +296,51 @@ def slices(
return fig
-def _get_slice_range(position: int, n_slices: int, n_total):
+def _get_slice_range(position: int, num_slices: int, n_total):
"""Helper function for `slices`. Returns the range of slices to be displayed around the given position."""
- start_idx = position - n_slices // 2
+ start_idx = position - num_slices // 2
end_idx = (
- position + n_slices // 2 if n_slices % 2 == 0 else position + n_slices // 2 + 1
+ position + num_slices // 2
+ if num_slices % 2 == 0
+ else position + num_slices // 2 + 1
)
slice_idxs = np.arange(start_idx, end_idx)
if slice_idxs[0] < 0:
- slice_idxs = np.arange(0, n_slices)
+ slice_idxs = np.arange(0, num_slices)
elif slice_idxs[-1] > n_total:
- slice_idxs = np.arange(n_total - n_slices, n_total)
+ slice_idxs = np.arange(n_total - num_slices, n_total)
return slice_idxs
def slicer(
- vol: np.ndarray,
- axis: int = 0,
- cmap: str = "viridis",
- vmin: float = None,
- vmax: float = None,
- img_height: int = 3,
- img_width: int = 3,
- show_position: bool = False,
+ volume: np.ndarray,
+ slice_axis: int = 0,
+ color_map: str = "magma",
+ value_min: float = None,
+ value_max: float = None,
+ image_height: int = 3,
+ image_width: int = 3,
+ display_positions: bool = False,
interpolation: Optional[str] = None,
- img_size=None,
- cbar: bool = False,
- **imshow_kwargs,
+ image_size=None,
+ color_bar: bool = False,
+ **matplotlib_imshow_kwargs,
) -> widgets.interactive:
"""Interactive widget for visualizing slices of a 3D volume.
Args:
- vol (np.ndarray): The 3D volume to be sliced.
- axis (int, optional): Specifies the axis, or dimension, along which to slice. Defaults to 0.
- cmap (str, optional): Specifies the color map for the image. Defaults to "viridis".
- vmin (float, optional): Together with vmax define the data range the colormap covers. By default colormap covers the full range. Defaults to None.
- vmax (float, optional): Together with vmin define the data range the colormap covers. By default colormap covers the full range. Defaults to None
- img_height (int, optional): Height of the figure. Defaults to 3.
- img_width (int, optional): Width of the figure. Defaults to 3.
- show_position (bool, optional): If True, displays the position of the slices. Defaults to False.
+ volume (np.ndarray): The 3D volume to be sliced.
+ slice_axis (int, optional): Specifies the axis, or dimension, along which to slice. Defaults to 0.
+ color_map (str, optional): Specifies the color map for the image. Defaults to "viridis".
+ value_min (float, optional): Together with value_max define the data range the colormap covers. By default colormap covers the full range. Defaults to None.
+ value_max (float, optional): Together with value_min define the data range the colormap covers. By default colormap covers the full range. Defaults to None
+ image_height (int, optional): Height of the figure. Defaults to 3.
+ image_width (int, optional): Width of the figure. Defaults to 3.
+ display_positions (bool, optional): If True, displays the position of the slices. Defaults to False.
interpolation (str, optional): Specifies the interpolation method for the image. Defaults to None.
- cbar (bool, optional): Adds a colorbar for the corresponding colormap and data range. Defaults to False.
+ color_bar (bool, optional): Adds a colorbar for the corresponding colormap and data range. Defaults to False.
Returns:
slicer_obj (widgets.interactive): The interactive widget for visualizing slices of a 3D volume.
@@ -328,98 +355,98 @@ def slicer(
"""
- if img_size:
- img_height = img_size
- img_width = img_size
+ if image_size:
+ image_height = image_size
+ image_width = image_size
# Create the interactive widget
- def _slicer(position):
- fig = slices(
- vol,
- axis=axis,
- cmap=cmap,
- vmin=vmin,
- vmax=vmax,
- img_height=img_height,
- img_width=img_width,
- show_position=show_position,
+ def _slicer(slice_positions):
+ fig = slices_grid(
+ volume,
+ slice_axis=slice_axis,
+ color_map=color_map,
+ value_min=value_min,
+ value_max=value_max,
+ image_height=image_height,
+ image_width=image_width,
+ display_positions=display_positions,
interpolation=interpolation,
- position=position,
- n_slices=1,
- show=True,
- cbar=cbar,
- **imshow_kwargs,
+ slice_positions=slice_positions,
+ num_slices=1,
+ display_figure=True,
+ color_bar=color_bar,
+ **matplotlib_imshow_kwargs,
)
return fig
position_slider = widgets.IntSlider(
- value=vol.shape[axis] // 2,
+ value=volume.shape[slice_axis] // 2,
min=0,
- max=vol.shape[axis] - 1,
+ max=volume.shape[slice_axis] - 1,
description="Slice",
continuous_update=True,
)
- slicer_obj = widgets.interactive(_slicer, position=position_slider)
+ slicer_obj = widgets.interactive(_slicer, slice_positions=position_slider)
slicer_obj.layout = widgets.Layout(align_items="flex-start")
return slicer_obj
-def orthogonal(
- vol: np.ndarray,
- cmap: str = "viridis",
- vmin: float = None,
- vmax: float = None,
- img_height: int = 3,
- img_width: int = 3,
- show_position: bool = False,
+def slicer_orthogonal(
+ volume: np.ndarray,
+ color_map: str = "magma",
+ value_min: float = None,
+ value_max: float = None,
+ image_height: int = 3,
+ image_width: int = 3,
+ display_positions: bool = False,
interpolation: Optional[str] = None,
- img_size=None,
+ image_size=None,
):
"""Interactive widget for visualizing orthogonal slices of a 3D volume.
Args:
- vol (np.ndarray): The 3D volume to be sliced.
- cmap (str, optional): Specifies the color map for the image. Defaults to "viridis".
- vmin (float, optional): Together with vmax define the data range the colormap covers. By default colormap covers the full range. Defaults to None.
- vmax (float, optional): Together with vmin define the data range the colormap covers. By default colormap covers the full range. Defaults to None
- img_height (int, optional): Height of the figure.
- img_width (int, optional): Width of the figure.
- show_position (bool, optional): If True, displays the position of the slices. Defaults to False.
+ volume (np.ndarray): The 3D volume to be sliced.
+ color_map (str, optional): Specifies the color map for the image. Defaults to "viridis".
+ value_min (float, optional): Together with value_max define the data range the colormap covers. By default colormap covers the full range. Defaults to None.
+ value_max (float, optional): Together with value_min define the data range the colormap covers. By default colormap covers the full range. Defaults to None
+ image_height (int, optional): Height of the figure.
+ image_width (int, optional): Width of the figure.
+ display_positions (bool, optional): If True, displays the position of the slices. Defaults to False.
interpolation (str, optional): Specifies the interpolation method for the image. Defaults to None.
Returns:
- orthogonal_obj (widgets.HBox): The interactive widget for visualizing orthogonal slices of a 3D volume.
+ slicer_orthogonal_obj (widgets.HBox): The interactive widget for visualizing orthogonal slices of a 3D volume.
Example:
```python
import qim3d
vol = qim3d.examples.fly_150x256x256
- qim3d.viz.orthogonal(vol, cmap="magma")
+ qim3d.viz.slicer_orthogonal(vol, color_map="magma")
```
- 
+ 
"""
- if img_size:
- img_height = img_size
- img_width = img_size
-
- get_slicer_for_axis = lambda axis: slicer(
- vol,
- axis=axis,
- cmap=cmap,
- vmin=vmin,
- vmax=vmax,
- img_height=img_height,
- img_width=img_width,
- show_position=show_position,
+ if image_size:
+ image_height = image_size
+ image_width = image_size
+
+ get_slicer_for_axis = lambda slice_axis: slicer(
+ volume,
+ slice_axis=slice_axis,
+ color_map=color_map,
+ value_min=value_min,
+ value_max=value_max,
+ image_height=image_height,
+ image_width=image_width,
+ display_positions=display_positions,
interpolation=interpolation,
)
- z_slicer = get_slicer_for_axis(axis=0)
- y_slicer = get_slicer_for_axis(axis=1)
- x_slicer = get_slicer_for_axis(axis=2)
+ z_slicer = get_slicer_for_axis(slice_axis=0)
+ y_slicer = get_slicer_for_axis(slice_axis=1)
+ x_slicer = get_slicer_for_axis(slice_axis=2)
z_slicer.children[0].description = "Z"
y_slicer.children[0].description = "Y"
@@ -428,29 +455,29 @@ def orthogonal(
return widgets.HBox([z_slicer, y_slicer, x_slicer])
-def interactive_fade_mask(
- vol: np.ndarray,
+def fade_mask(
+ volume: np.ndarray,
axis: int = 0,
- cmap: str = "viridis",
- vmin: float = None,
- vmax: float = None,
+ color_map: str = "magma",
+ value_min: float = None,
+ value_max: float = None,
):
"""Interactive widget for visualizing the effect of edge fading on a 3D volume.
This can be used to select the best parameters before applying the mask.
Args:
- vol (np.ndarray): The volume to apply edge fading to.
+ volume (np.ndarray): The volume to apply edge fading to.
axis (int, optional): The axis along which to apply the fading. Defaults to 0.
- cmap (str, optional): Specifies the color map for the image. Defaults to "viridis".
- vmin (float, optional): Together with vmax define the data range the colormap covers. By default colormap covers the full range. Defaults to None.
- vmax (float, optional): Together with vmin define the data range the colormap covers. By default colormap covers the full range. Defaults to None
+ color_map (str, optional): Specifies the color map for the image. Defaults to "viridis".
+ value_min (float, optional): Together with value_max define the data range the colormap covers. By default colormap covers the full range. Defaults to None.
+ value_max (float, optional): Together with value_min define the data range the colormap covers. By default colormap covers the full range. Defaults to None
Example:
```python
import qim3d
vol = qim3d.examples.cement_128x128x128
- qim3d.viz.interactive_fade_mask(vol)
+ qim3d.viz.fade_mask(vol)
```
@@ -460,58 +487,62 @@ def interactive_fade_mask(
def _slicer(position, decay_rate, ratio, geometry, invert):
fig, axes = plt.subplots(1, 3, figsize=(9, 3))
- slice_img = vol[position, :, :]
- # If vmin is higher than the highest value in the image ValueError is raised
+ slice_img = volume[position, :, :]
+ # If value_min is higher than the highest value in the image ValueError is raised
# We don't want to override the values because next slices might be okay
- new_vmin = (
+ new_value_min = (
None
- if (isinstance(vmin, (float, int)) and vmin > np.max(slice_img))
- else vmin
+ if (isinstance(value_min, (float, int)) and value_min > np.max(slice_img))
+ else value_min
)
- new_vmax = (
+ new_value_max = (
None
- if (isinstance(vmax, (float, int)) and vmax < np.min(slice_img))
- else vmax
+ if (isinstance(value_max, (float, int)) and value_max < np.min(slice_img))
+ else value_max
)
- axes[0].imshow(slice_img, cmap=cmap, vmin=new_vmin, vmax=new_vmax)
+ axes[0].imshow(
+ slice_img, cmap=color_map, value_min=new_value_min, value_max=new_value_max
+ )
axes[0].set_title("Original")
axes[0].axis("off")
mask = qim3d.processing.operations.fade_mask(
- np.ones_like(vol),
+ np.ones_like(volume),
decay_rate=decay_rate,
ratio=ratio,
geometry=geometry,
axis=axis,
invert=invert,
)
- axes[1].imshow(mask[position, :, :], cmap=cmap)
+ axes[1].imshow(mask[position, :, :], cmap=color_map)
axes[1].set_title("Mask")
axes[1].axis("off")
- masked_vol = qim3d.processing.operations.fade_mask(
- vol,
+ masked_volume = qim3d.processing.operations.fade_mask(
+ volume,
decay_rate=decay_rate,
ratio=ratio,
geometry=geometry,
axis=axis,
invert=invert,
)
- # If vmin is higher than the highest value in the image ValueError is raised
+ # If value_min is higher than the highest value in the image ValueError is raised
# We don't want to override the values because next slices might be okay
- slice_img = masked_vol[position, :, :]
- new_vmin = (
+ slice_img = masked_volume[position, :, :]
+ new_value_min = (
None
- if (isinstance(vmin, (float, int)) and vmin > np.max(slice_img))
- else vmin
+ if (isinstance(value_min, (float, int)) and value_min > np.max(slice_img))
+ else value_min
)
- new_vmax = (
+ new_value_max = (
None
- if (isinstance(vmax, (float, int)) and vmax < np.min(slice_img))
- else vmax
+ if (isinstance(value_max, (float, int)) and value_max < np.min(slice_img))
+ else value_max
+ )
+ axes[2].imshow(
+ slice_img, cmap=color_map, vmin=new_value_min, vmax=new_value_max
)
- axes[2].imshow(slice_img, cmap=cmap, vmin=new_vmin, vmax=new_vmax)
axes[2].set_title("Masked")
axes[2].axis("off")
@@ -524,9 +555,9 @@ def interactive_fade_mask(
)
position_slider = widgets.IntSlider(
- value=vol.shape[0] // 2,
+ value=volume.shape[0] // 2,
min=0,
- max=vol.shape[0] - 1,
+ max=volume.shape[0] - 1,
description="Slice",
continuous_update=False,
)
@@ -659,13 +690,13 @@ def chunks(zarr_path: str, **kwargs):
viz_widget = widgets.Output()
with viz_widget:
viz_widget.clear_output(wait=True)
- fig = qim3d.viz.slices(chunk, **kwargs)
+ fig = qim3d.viz.slices_grid_grid(chunk, **kwargs)
display(fig)
- elif visualization_method == "vol":
+ elif visualization_method == "volume":
viz_widget = widgets.Output()
with viz_widget:
viz_widget.clear_output(wait=True)
- out = qim3d.viz.vol(chunk, show=False, **kwargs)
+ out = qim3d.viz.volumetric(chunk, show=False, **kwargs)
display(out)
else:
log.info(f"Invalid visualization method: {visualization_method}")
@@ -716,7 +747,7 @@ def chunks(zarr_path: str, **kwargs):
)
method_dropdown = widgets.Dropdown(
- options=["slicer", "slices", "vol"],
+ options=["slicer", "slices", "volume"],
value="slicer",
description="Visualization",
style={"description_width": description_width, "text_align": "left"},
@@ -815,7 +846,7 @@ def chunks(zarr_path: str, **kwargs):
def histogram(
- vol: np.ndarray,
+ volume: np.ndarray,
bins: Union[int, str] = "auto",
slice_idx: Union[int, str] = None,
axis: int = 0,
@@ -833,11 +864,11 @@ def histogram(
):
"""
Plots a histogram of voxel intensities from a 3D volume, with options to show a specific slice or the entire volume.
-
+
Utilizes [seaborn.histplot](https://seaborn.pydata.org/generated/seaborn.histplot.html) for visualization.
Args:
- vol (np.ndarray): A 3D NumPy array representing the volume to be visualized.
+ volume (np.ndarray): A 3D NumPy array representing the volume to be visualized.
bins (Union[int, str], optional): Number of histogram bins or a binning strategy (e.g., "auto"). Default is "auto".
axis (int, optional): Axis along which to take a slice. Default is 0.
slice_idx (Union[int, str], optional): Specifies the slice to visualize. If an integer, it represents the slice index along the selected axis.
@@ -879,24 +910,24 @@ def histogram(
"""
- if not (0 <= axis < vol.ndim):
- raise ValueError(f"Axis must be an integer between 0 and {vol.ndim - 1}.")
+ if not (0 <= axis < volume.ndim):
+ raise ValueError(f"Axis must be an integer between 0 and {volume.ndim - 1}.")
if slice_idx == "middle":
- slice_idx = vol.shape[axis] // 2
+ slice_idx = volume.shape[axis] // 2
if slice_idx:
- if 0 <= slice_idx < vol.shape[axis]:
- img_slice = np.take(vol, indices=slice_idx, axis=axis)
+ if 0 <= slice_idx < volume.shape[axis]:
+ img_slice = np.take(volume, indices=slice_idx, axis=axis)
data = img_slice.ravel()
title = f"Intensity histogram of slice #{slice_idx} {img_slice.shape} along axis {axis}"
else:
raise ValueError(
- f"Slice index out of range. Must be between 0 and {vol.shape[axis] - 1}."
+ f"Slice index out of range. Must be between 0 and {volume.shape[axis] - 1}."
)
else:
- data = vol.ravel()
- title = f"Intensity histogram for whole volume {vol.shape}"
+ data = volume.ravel()
+ title = f"Intensity histogram for whole volume {volume.shape}"
fig, ax = plt.subplots(figsize=figsize)
diff --git a/qim3d/viz/detection.py b/qim3d/viz/_detection.py
similarity index 97%
rename from qim3d/viz/detection.py
rename to qim3d/viz/_detection.py
index fcf493cd..a0926105 100644
--- a/qim3d/viz/detection.py
+++ b/qim3d/viz/_detection.py
@@ -1,5 +1,5 @@
import matplotlib.pyplot as plt
-from qim3d.utils.logger import log
+from qim3d.utils._logger import log
import numpy as np
import ipywidgets as widgets
from IPython.display import clear_output, display
@@ -29,7 +29,7 @@ def circles(blobs, vol, alpha=0.5, color="#ff9900", **kwargs):
def _slicer(z_slice):
clear_output(wait=True)
- fig = qim3d.viz.slices(
+ fig = qim3d.viz.slices_grid(
vol,
n_slices=1,
position=z_slice,
diff --git a/qim3d/viz/k3d.py b/qim3d/viz/_k3d.py
similarity index 85%
rename from qim3d/viz/k3d.py
rename to qim3d/viz/_k3d.py
index c3018e08..b80e9556 100644
--- a/qim3d/viz/k3d.py
+++ b/qim3d/viz/_k3d.py
@@ -10,17 +10,17 @@ Volumetric visualization using K3D
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.colors import Colormap
-from qim3d.utils.logger import log
-from qim3d.utils.misc import downscale_img, scale_to_float16
+from qim3d.utils._logger import log
+from qim3d.utils._misc import downscale_img, scale_to_float16
-def vol(
+def volumetric(
img,
aspectmode="data",
show=True,
save=False,
grid_visible=False,
- cmap=None,
+ color_map='magma',
constant_opacity=False,
vmin=None,
vmax=None,
@@ -43,8 +43,8 @@ def vol(
If a string is provided, it's interpreted as the file path where the HTML
file will be saved. Defaults to False.
grid_visible (bool, optional): If True, the grid is visible in the plot. Defaults to False.
- cmap (str or matplotlib.colors.Colormap or list, optional): The color map to be used for the volume rendering. If a string is passed, it should be a matplotlib colormap name. Defaults to None.
- constant_opacity (bool, float): Set to True if doing an object label visualization with a corresponding cmap; otherwise, the plot may appear poorly. Defaults to False.
+ color_map (str or matplotlib.colors.Colormap or list, optional): The color map to be used for the volume rendering. If a string is passed, it should be a matplotlib colormap name. Defaults to None.
+ constant_opacity (bool, float): Set to True if doing an object label visualization with a corresponding color_map; otherwise, the plot may appear poorly. Defaults to False.
vmin (float, optional): Together with vmax defines the data range the colormap covers. By default colormap covers the full range. Defaults to None.
vmax (float, optional): Together with vmin defines the data range the colormap covers. By default colormap covers the full range. Defaults to None
samples (int, optional): The number of samples to be used for the volume rendering in k3d. Defaults to 512.
@@ -60,7 +60,7 @@ def vol(
ValueError: If `aspectmode` is not `'data'` or `'cube'`.
Tip:
- The function can be used for object label visualization using a `cmap` created with `qim3d.viz.colormaps.objects` along with setting `objects=True`. The latter ensures appropriate rendering.
+ The function can be used for object label visualization using a `color_map` created with `qim3d.viz.colormaps.objects` along with setting `objects=True`. The latter ensures appropriate rendering.
Example:
Display a volume inline:
@@ -69,7 +69,7 @@ def vol(
import qim3d
vol = qim3d.examples.bone_128x128x128
- qim3d.viz.vol(vol)
+ qim3d.viz.volumetric(vol)
```
<iframe src="https://platform.qim.dk/k3d/fima-bone_128x128x128-20240221113459.html" width="100%" height="500" frameborder="0"></iframe>
@@ -78,7 +78,7 @@ def vol(
```python
import qim3d
vol = qim3d.examples.bone_128x128x128
- plot = qim3d.viz.vol(vol, show=False, save="plot.html")
+ plot = qim3d.viz.volumetric(vol, show=False, save="plot.html")
```
"""
@@ -129,21 +129,21 @@ def vol(
if vmax:
color_range[1] = vmax
- # Handle the different formats that cmap can take
- if cmap:
- if isinstance(cmap, str):
- cmap = plt.get_cmap(cmap) # Convert to Colormap object
- if isinstance(cmap, Colormap):
- # Convert to the format of cmap required by k3d.volume
- attr_vals = np.linspace(0.0, 1.0, num=cmap.N)
- RGB_vals = cmap(np.arange(0, cmap.N))[:, :3]
- cmap = np.column_stack((attr_vals, RGB_vals)).tolist()
+ # Handle the different formats that color_map can take
+ if color_map:
+ if isinstance(color_map, str):
+ color_map = plt.get_cmap(color_map) # Convert to Colormap object
+ if isinstance(color_map, Colormap):
+ # Convert to the format of color_map required by k3d.volume
+ attr_vals = np.linspace(0.0, 1.0, num=color_map.N)
+ RGB_vals = color_map(np.arange(0, color_map.N))[:, :3]
+ color_map = np.column_stack((attr_vals, RGB_vals)).tolist()
# Default k3d.volume settings
opacity_function = []
interpolation = True
if constant_opacity:
- # without these settings, the plot will look bad when cmap is created with qim3d.viz.colormaps.objects
+ # without these settings, the plot will look bad when color_map is created with qim3d.viz.colormaps.objects
opacity_function = [0.0, float(constant_opacity), 1.0, float(constant_opacity)]
interpolation = False
@@ -155,7 +155,7 @@ def vol(
if aspectmode.lower() == "data"
else None
),
- color_map=cmap,
+ color_map=color_map,
samples=samples,
color_range=color_range,
opacity_function=opacity_function,
diff --git a/qim3d/viz/layers2d.py b/qim3d/viz/_layers2d.py
similarity index 100%
rename from qim3d/viz/layers2d.py
rename to qim3d/viz/_layers2d.py
diff --git a/qim3d/viz/local_thickness_.py b/qim3d/viz/_local_thickness.py
similarity index 99%
rename from qim3d/viz/local_thickness_.py
rename to qim3d/viz/_local_thickness.py
index e1195e7d..c07438ee 100644
--- a/qim3d/viz/local_thickness_.py
+++ b/qim3d/viz/_local_thickness.py
@@ -1,4 +1,4 @@
-from qim3d.utils.logger import log
+from qim3d.utils._logger import log
import numpy as np
import matplotlib.pyplot as plt
from typing import Optional, Union, Tuple
diff --git a/qim3d/viz/metrics.py b/qim3d/viz/_metrics.py
similarity index 99%
rename from qim3d/viz/metrics.py
rename to qim3d/viz/_metrics.py
index 7cbd08ea..53a7f3a6 100644
--- a/qim3d/viz/metrics.py
+++ b/qim3d/viz/_metrics.py
@@ -4,7 +4,7 @@ import numpy as np
import matplotlib.pyplot as plt
from matplotlib.colors import LinearSegmentedColormap
from matplotlib import colormaps
-from qim3d.utils.logger import log
+from qim3d.utils._logger import log
def plot_metrics(
diff --git a/qim3d/viz/preview.py b/qim3d/viz/_preview.py
similarity index 100%
rename from qim3d/viz/preview.py
rename to qim3d/viz/_preview.py
diff --git a/qim3d/viz/structure_tensor.py b/qim3d/viz/_structure_tensor.py
similarity index 99%
rename from qim3d/viz/structure_tensor.py
rename to qim3d/viz/_structure_tensor.py
index 21b0e24d..63d141c4 100644
--- a/qim3d/viz/structure_tensor.py
+++ b/qim3d/viz/_structure_tensor.py
@@ -4,7 +4,7 @@ import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec
import ipywidgets as widgets
import logging
-from qim3d.utils.logger import log
+from qim3d.utils._logger import log
previous_logging_level = logging.getLogger().getEffectiveLevel()
diff --git a/qim3d/viz/colormaps/__init__.py b/qim3d/viz/colormaps/__init__.py
new file mode 100644
index 00000000..9807422f
--- /dev/null
+++ b/qim3d/viz/colormaps/__init__.py
@@ -0,0 +1,2 @@
+from ._segmentation import segmentation
+from ._qim_colors import qim
\ No newline at end of file
diff --git a/qim3d/viz/colormaps/_qim_colors.py b/qim3d/viz/colormaps/_qim_colors.py
new file mode 100644
index 00000000..429151e1
--- /dev/null
+++ b/qim3d/viz/colormaps/_qim_colors.py
@@ -0,0 +1,24 @@
+from matplotlib import colormaps
+from matplotlib.colors import LinearSegmentedColormap
+
+
+qim = LinearSegmentedColormap.from_list(
+ "qim",
+ [
+ (0.6, 0.0, 0.0), # 990000
+ (1.0, 0.6, 0.0), # ff9900
+ ],
+)
+"""
+Defines colormap in QIM logo colors. Can be accessed as module attribute or easily by ```cmap = 'qim'```
+
+Example:
+ ```python
+
+ import qim3d
+
+ display(qim3d.viz.colormaps.qim)
+ ```
+ 
+"""
+colormaps.register(qim)
diff --git a/qim3d/viz/colormaps.py b/qim3d/viz/colormaps/_segmentation.py
similarity index 81%
rename from qim3d/viz/colormaps.py
rename to qim3d/viz/colormaps/_segmentation.py
index 807a0838..b6ee2f88 100644
--- a/qim3d/viz/colormaps.py
+++ b/qim3d/viz/colormaps/_segmentation.py
@@ -7,7 +7,6 @@ from typing import Union, Tuple
import numpy as np
import math
from matplotlib.colors import LinearSegmentedColormap
-from matplotlib import colormaps
def rearrange_colors(randRGBcolors_old, min_dist=0.5):
@@ -33,8 +32,8 @@ def rearrange_colors(randRGBcolors_old, min_dist=0.5):
return randRGBcolors_new
-def objects(
- nlabels: int,
+def segmentation(
+ num_labels: int,
style: str = "bright",
first_color_background: bool = True,
last_color_background: bool = False,
@@ -46,7 +45,7 @@ def objects(
Creates a random colormap to be used together with matplotlib. Useful for segmentation tasks
Args:
- nlabels (int): Number of labels (size of colormap).
+ num_labels (int): Number of labels (size of colormap).
style (str, optional): 'bright' for strong colors, 'soft' for pastel colors, 'earth' for yellow/green/blue colors, 'ocean' for blue/purple/pink colors. Defaults to 'bright'.
first_color_background (bool, optional): If True, the first color is used as background. Defaults to True.
last_color_background (bool, optional): If True, the last color is used as background. Defaults to False.
@@ -62,10 +61,10 @@ def objects(
```python
import qim3d
- cmap_bright = qim3d.viz.colormaps.objects(nlabels=100, style = 'bright', first_color_background=True, background_color="black", min_dist=0.7)
- cmap_soft = qim3d.viz.colormaps.objects(nlabels=100, style = 'soft', first_color_background=True, background_color="black", min_dist=0.2)
- cmap_earth = qim3d.viz.colormaps.objects(nlabels=100, style = 'earth', first_color_background=True, background_color="black", min_dist=0.8)
- cmap_ocean = qim3d.viz.colormaps.objects(nlabels=100, style = 'ocean', first_color_background=True, background_color="black", min_dist=0.9)
+ cmap_bright = qim3d.viz.colormaps.objects(num_labels=100, style = 'bright', first_color_background=True, background_color="black", min_dist=0.7)
+ cmap_soft = qim3d.viz.colormaps.objects(num_labels=100, style = 'soft', first_color_background=True, background_color="black", min_dist=0.2)
+ cmap_earth = qim3d.viz.colormaps.objects(num_labels=100, style = 'earth', first_color_background=True, background_color="black", min_dist=0.8)
+ cmap_ocean = qim3d.viz.colormaps.objects(num_labels=100, style = 'ocean', first_color_background=True, background_color="black", min_dist=0.9)
display(cmap_bright)
display(cmap_soft)
@@ -89,7 +88,7 @@ def objects(
Tip:
It can be easily used when calling visualization functions as
```python
- qim3d.viz.slices(segmented_volume, cmap = 'objects')
+ qim3d.viz.slices_grid(segmented_volume, cmap = 'objects')
```
which automatically detects number of unique classes
and creates the colormap object with defualt arguments.
@@ -116,8 +115,8 @@ def objects(
f'Invalid color name "{background_color}". Please choose from {list(color_dict.keys())}.'
)
- # Add one to nlabels to include the background color
- nlabels += 1
+ # Add one to num_labels to include the background color
+ num_labels += 1
# Create a new random generator, to locally set seed
rng = np.random.default_rng(seed)
@@ -130,7 +129,7 @@ def objects(
rng.uniform(low=0.4, high=1),
rng.uniform(low=0.9, high=1),
)
- for i in range(nlabels)
+ for i in range(num_labels)
]
# Convert HSV list to RGB
@@ -150,7 +149,7 @@ def objects(
rng.uniform(low=low, high=high),
rng.uniform(low=low, high=high),
)
- for i in range(nlabels)
+ for i in range(num_labels)
]
# Generate color map for earthy colors, based on LAB
@@ -161,7 +160,7 @@ def objects(
rng.uniform(low=-120, high=70),
rng.uniform(low=-70, high=70),
)
- for i in range(nlabels)
+ for i in range(num_labels)
]
# Convert LAB list to RGB
@@ -177,7 +176,7 @@ def objects(
rng.uniform(low=-128, high=160),
rng.uniform(low=-128, high=0),
)
- for i in range(nlabels)
+ for i in range(num_labels)
]
# Convert LAB list to RGB
@@ -196,28 +195,8 @@ def objects(
randRGBcolors[-1] = background_color
# Create colormap
- objects = LinearSegmentedColormap.from_list("objects", randRGBcolors, N=nlabels)
+ objects = LinearSegmentedColormap.from_list("objects", randRGBcolors, N=num_labels)
return objects
-qim = LinearSegmentedColormap.from_list(
- "qim",
- [
- (0.6, 0.0, 0.0), # 990000
- (1.0, 0.6, 0.0), # ff9900
- ],
-)
-"""
-Defines colormap in QIM logo colors. Can be accessed as module attribute or easily by ```cmap = 'qim'```
-
-Example:
- ```python
-
- import qim3d
-
- display(qim3d.viz.colormaps.qim)
- ```
- 
-"""
-colormaps.register(qim)
diff --git a/qim3d/viz/itk_vtk_viewer/run.py b/qim3d/viz/itk_vtk_viewer/run.py
index 8ff029fc..8fa5e6b8 100644
--- a/qim3d/viz/itk_vtk_viewer/run.py
+++ b/qim3d/viz/itk_vtk_viewer/run.py
@@ -3,7 +3,7 @@ import platform
from pathlib import Path
import os
import qim3d.utils
-from qim3d.utils.logger import log
+from qim3d.utils._logger import log
# from .helpers import get_qim_dir, get_nvm_dir, get_viewer_binaries, get_viewer_dir, get_node_binaries_dir, NotInstalledError, SOURCE_FNM
from .helpers import *
--
GitLab