napari_ndev.widgets._utilities_container
#
UtilitiesContainer
#
Bases: ScrollableContainer
A widget to work with images and labels in the napari viewer.
Parameters:
Attributes:
-
_viewer
(Viewer
) –The napari viewer instance.
-
_image_save_dims
(str or None
) –The dimension order for saving images.
-
_label_save_dims
(str or None
) –The dimension order for saving labels.
-
_p_sizes
(PhysicalPixelSizes
) –The physical pixel sizes for the image.
-
_files
(FileEdit
) –Widget for selecting file(s).
-
_open_image_button
(PushButton
) –Button for opening images.
-
_save_directory
(FileEdit
) –Widget for selecting the save directory.
-
_save_name
(LineEdit
) –Widget for entering the file save name.
-
_metadata_from_selected_layer
(PushButton
) –Button for updating metadata from the selected layer.
-
_dim_order
(LineEdit
) –Widget for entering the dimension order.
-
_channel_names
(LineEdit
) –Widget for entering the channel names.
-
_physical_pixel_sizes_z
(FloatSpinBox
) –Widget for entering the Z pixel size in micrometers.
-
_physical_pixel_sizes_y
(FloatSpinBox
) –Widget for entering the Y pixel size in micrometers.
-
_physical_pixel_sizes_x
(FloatSpinBox
) –Widget for entering the X pixel size in micrometers.
-
_image_layer
(Select
) –Widget for selecting the image layer.
-
_concatenate_image_files
(CheckBox
) –Checkbox for concatenating image files.
-
_concatenate_image_layers
(CheckBox
) –Checkbox for concatenating image layers.
-
_save_image_button
(PushButton
) –Button for saving images.
-
_labels_layer
(Widget
) –Widget for working with labels layer.
-
_save_labels_button
(PushButton
) –Button for saving labels.
-
_shapes_layer
(Widget
) –Widget for working with shapes layer.
-
_save_shapes_button
(PushButton
) –Button for saving shapes as labels.
-
_results
(TextEdit
) –Widget for displaying information.
Methods:
-
_update_metadata
–Update the metadata based on the given image.
-
update_metadata_from_file
–Update the metadata from the selected file.
-
update_metadata_from_layer
–Update the metadata from the selected layer.
-
open_images
–Open the selected images in the napari viewer.
-
concatenate_images
–Concatenate the image data based on the selected options.
-
p_sizes
–Get the physical pixel sizes.
-
_get_save_loc
–Get the save location based on the parent directory.
-
_common_save_logic
–Common logic for saving data as OME-TIFF.
-
save_ome_tiff
–Save the concatenated image data as OME-TIFF.
-
save_labels
–Save the labels data.
-
save_shapes_as_labels
–Save the shapes data as labels.
Source code in src/napari_ndev/widgets/_utilities_container.py
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p_sizes
property
#
p_sizes
Get the physical pixel sizes.
Returns:
-
PhysicalPixelSizes
–The physical pixel sizes.
__init__
#
__init__(viewer=None)
Initialize the UtilitiesContainer widget.
Parameters:
Source code in src/napari_ndev/widgets/_utilities_container.py
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_common_save_logic
#
_common_save_logic(data, uri, dim_order, channel_names, image_name, result_str)
Save data as OME-TIFF with bioio based on common logic.
Converts labels to np.int32 if np.int64 is detected, due to bioio not supporting np.int64 labels, even though napari and other libraries generate np.int64 labels.
Parameters:
-
data
#ndarray
) –The data to save.
-
uri
#Path
) –The URI to save the data to.
-
dim_order
#str
) –The dimension order.
-
channel_names
#list[str]
) –The channel names saved to OME metadata
-
image_name
#str | list[str | None] | None
) –The image name saved to OME metadata
-
result_str
#str
) –The string used for the result widget.
Source code in src/napari_ndev/widgets/_utilities_container.py
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_connect_events
#
_connect_events()
Connect the events of the widgets to respective methods.
Source code in src/napari_ndev/widgets/_utilities_container.py
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_get_save_loc
#
_get_save_loc(root_dir, parent, file_name)
Get the save location based on the parent directory.
Parameters:
-
root_dir
#Path
) –The root directory.
-
parent
#str
) –The parent directory. eg. 'Image', 'Labels', 'ShapesAsLabels'
-
file_name
#str
) –The file name.
Returns:
-
Path
–The save location. root_dir / parent / file_name
Source code in src/napari_ndev/widgets/_utilities_container.py
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_init_layout
#
_init_layout()
Initialize the layout of the widget.
Source code in src/napari_ndev/widgets/_utilities_container.py
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_init_open_image_container
#
_init_open_image_container()
Initialize the open image container.
Source code in src/napari_ndev/widgets/_utilities_container.py
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_init_save_layers_container
#
_init_save_layers_container()
Initialize the container to save images, labels, and shapes.
Source code in src/napari_ndev/widgets/_utilities_container.py
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_init_save_name_container
#
_init_save_name_container()
Initialize the save name container.
Source code in src/napari_ndev/widgets/_utilities_container.py
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_init_scene_container
#
_init_scene_container()
Initialize the scene container, allowing scene saving.
Source code in src/napari_ndev/widgets/_utilities_container.py
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_init_widgets
#
_init_widgets()
Initialize widgets.
Source code in src/napari_ndev/widgets/_utilities_container.py
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_update_metadata_from_Image
#
_update_metadata_from_Image(img, update_channel_names=True, update_scale=True)
Update the metadata based on the given image.
Parameters:
-
img
#BioImage
) –The image from which to update the metadata.
-
update_channel_names
#bool
, default:True
) –Update the channel names, by default True.
-
update_scale
#bool
, default:True
) –Update the scale, by default True.
Source code in src/napari_ndev/widgets/_utilities_container.py
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append_scene_to_name
#
append_scene_to_name()
Append the scene to the save name.
Source code in src/napari_ndev/widgets/_utilities_container.py
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batch_concatenate_files
#
batch_concatenate_files()
Concatenate files in the selected directory.
Save the concatenated files as OME-TIFF, then select the next set of files in the directory to be concatenated. This is done by iterating over the remaining files in the directory based on the number of files selected. The files are sorted alphabetically and numerically. The files will be concatenated until no more files are left in the parent directory.
Source code in src/napari_ndev/widgets/_utilities_container.py
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canvas_export_figure
#
canvas_export_figure()
Export the current canvas figure to the save directory.
Source code in src/napari_ndev/widgets/_utilities_container.py
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canvas_screenshot
#
canvas_screenshot()
Export the current canvas screenshot to the save directory.
Source code in src/napari_ndev/widgets/_utilities_container.py
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concatenate_files
#
concatenate_files(files)
Concatenate the image data from the selected files.
Removes "empty" channels, which are channels with no values above 0. This is present in some microscope formats where it will image in RGB, and then leave empty channels not represented by the color channels.
Does not currently handle scenes.
Parameters:
-
files
#str or Path or list of str or Path
) –The file(s) to concatenate.
Returns:
-
ndarray
–The concatenated image data.
Source code in src/napari_ndev/widgets/_utilities_container.py
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concatenate_layers
#
concatenate_layers(layers)
Concatenate the image data from the selected layers.
Adapts all layers to 5D arrays for compatibility with image dims. If the layer is a shapes layer, it will look for a corresponding image layer to get the dimensions for the shapes layer.
Parameters:
-
layers
#napari.layers.Image or list of napari.layers.Image
) –The selected image layers.
Returns:
-
ndarray
–The concatenated image data.
Source code in src/napari_ndev/widgets/_utilities_container.py
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open_images
#
open_images()
Open the selected images in the napari viewer with napari-ndev.
Source code in src/napari_ndev/widgets/_utilities_container.py
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rescale_by
#
rescale_by()
Rescale the selected layers based on the given scale.
Source code in src/napari_ndev/widgets/_utilities_container.py
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save_files_as_ome_tiff
#
save_files_as_ome_tiff()
Save the selected files as OME-TIFF using BioImage.
Source code in src/napari_ndev/widgets/_utilities_container.py
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save_layers_as_ome_tiff
#
save_layers_as_ome_tiff()
Save the selected layers as OME-TIFF.
Determines types of layers and saves to corresponding directories.
Source code in src/napari_ndev/widgets/_utilities_container.py
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save_scenes_ome_tiff
#
save_scenes_ome_tiff()
Save selected scenes as OME-TIFF.
This method is intended to save scenes from a single file. The scenes are extracted based on the scenes_to_extract widget value, which is a list of scene indices. If the widget is left blank, then all scenes will be extracted.
Source code in src/napari_ndev/widgets/_utilities_container.py
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update_metadata_from_layer
#
update_metadata_from_layer()
Update metadata from the selected layer.
Expects images to be opened with napari-ndev reader.
Note:
This should also support napari-bioio in the future, when released.
Source code in src/napari_ndev/widgets/_utilities_container.py
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update_metadata_on_file_select
#
update_metadata_on_file_select()
Update self._save_name.value and metadata if selected.
Source code in src/napari_ndev/widgets/_utilities_container.py
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update_save_directory
#
update_save_directory()
Update the save directory based on the selected files.
Source code in src/napari_ndev/widgets/_utilities_container.py
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