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renamed equalization into contrast enhancement #6

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Nov 27, 2024
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renamed equalization into contrast enhancement #6

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90 changes: 45 additions & 45 deletions src/napari_tapenade_processing/_widget.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,8 +39,8 @@
compute_mask,
crop_array_using_mask,
crop_array_using_mask_from_files,
global_image_equalization,
local_image_equalization,
global_contrast_enhancement,
local_contrast_enhancement,
masked_gaussian_smoothing,
normalize_intensity,
reorganize_array_dimensions,
Expand Down Expand Up @@ -494,27 +494,27 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
labels=False,
)

# Image equalization
# Image contrast enhancement
if True:
self._local_global_equalization_checkbox = create_widget(
self._local_global_enhancement_checkbox = create_widget(
widget_type="CheckBox",
label="Perform global equalization",
label="Perform global contrast enhancement",
options={"value": False},
)

self._local_global_equalization_checkbox.clicked.connect(
self._update_local_global_equalization
self._local_global_enhancement_checkbox.clicked.connect(
self._update_local_global_enhancement
)

local_global_equalization_tooltip = (
"If checked, the equalization will be performed globally on the whole image.\n"
"If unchecked, the equalization will be performed locally in boxes of length (2*Box size)+1."
local_global_enhancement_tooltip = (
"If checked, the contrast enhancementll be performed globally on the whole image.\n"
"If unchecked, the contrast enhancementll be performed locally in boxes of length (2*Box size)+1."
)

local_global_equalization_container = (
local_global_enhancement_container = (
self._add_tooltip_button_to_container(
self._local_global_equalization_checkbox,
local_global_equalization_tooltip,
self._local_global_enhancement_checkbox,
local_global_enhancement_tooltip,
)
)

Expand All @@ -524,7 +524,7 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
options={"min": 3, "max": 25, "value": 10},
)
local_norm_box_size_tooltip = (
"Size of the box used for the image equalization\n"
"Size of the box used for the image contrast enhancement\n"
"A good default is ~ 3/2 * object radius."
)

Expand All @@ -535,27 +535,27 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
)
)

self._equalization_percentiles_slider = create_widget(
self._enhancement_percentiles_slider = create_widget(
widget_type="FloatRangeSlider",
label="Percentiles",
options={"min": 0, "max": 100, "value": [1, 99]},
)
equalization_percentiles_tooltip = (
"Percentiles used for the image equalization."
enhancement_percentiles_tooltip = (
"Percentiles used for the image contrast enhancement."
)

equalization_percentiles_container = (
enhancement_percentiles_container = (
self._add_tooltip_button_to_container(
self._equalization_percentiles_slider,
equalization_percentiles_tooltip,
self._enhancement_percentiles_slider,
enhancement_percentiles_tooltip,
)
)

self._image_equalization_container = Container(
self._contrast_enhancement_container = Container(
widgets=[
local_global_equalization_container,
local_global_enhancement_container,
self._local_norm_box_size_container,
equalization_percentiles_container,
enhancement_percentiles_container,
],
labels=False,
)
Expand Down Expand Up @@ -841,8 +841,8 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
"reorganize_array_dimensions": reorganize_array_dimensions,
"change_array_pixelsize": change_array_pixelsize,
"compute_mask": compute_mask,
"global_image_equalization": global_image_equalization,
"local_image_equalization": local_image_equalization,
"global_contrast_enhancement": global_contrast_enhancement,
"local_contrast_enhancement": local_contrast_enhancement,
"align_array_major_axis": align_array_major_axis,
"remove_labels_outside_of_mask": remove_labels_outside_of_mask,
"crop_array_using_mask": crop_array_using_mask,
Expand All @@ -861,8 +861,8 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
("Spectral filtering", self._spectral_filtering_container),
("Compute mask from image", self._compute_mask_container),
(
"Image equalization",
self._image_equalization_container,
"Image contrast enhancement",
self._contrast_enhancement_container,
),
("Intensity normalization", self._int_norm_container),
(
Expand Down Expand Up @@ -898,8 +898,8 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
("Spectral filtering", None),
("Compute mask from image", self._run_compute_mask),
(
"Image equalization",
self._run_image_equalization,
"Image contrast enhancement",
self._run_contrast_enhancement,
),
("Intensity normalization", self._run_normalize_intensity),
(
Expand Down Expand Up @@ -931,7 +931,7 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
"Change layer voxelsize": ["array"],
"Spectral filtering": [],
"Compute mask from image": ["image"],
"Image equalization": ["image", "mask"],
"Image contrast enhancement": ["image", "mask"],
"Intensity normalization": [
"image",
"ref_image",
Expand All @@ -956,8 +956,8 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
"reorganize_array_dimensions": "reorganized",
"change_array_pixelsize": "rescaled",
"compute_mask": "mask",
"global_image_equalization": "equalized",
"local_image_equalization": "equalized_locally",
"global_contrast_enhancement": "enhanced",
"local_contrast_enhancement": "enhanced_locally",
"align_array_major_axis": "aligned",
"remove_labels_outside_of_mask": "curated",
"crop_array_using_mask": "cropped",
Expand Down Expand Up @@ -1259,7 +1259,7 @@ def __init__(self, viewer: "napari.viewer.Viewer"):
self._disable_irrelevant_layers(0)
self._update_layer_combos()

def _update_local_global_equalization(self, event):
def _update_local_global_enhancement(self, event):
self._local_norm_box_size_container.enabled = not event

def _update_segment_stardist_thresholds(self, event):
Expand Down Expand Up @@ -1809,7 +1809,7 @@ def _run_compute_mask(self):
output_params_to_layer_names_and_types_dict=output_params_to_layer_names_and_types_dict,
)

def _run_image_equalization(self):
def _run_contrast_enhancement(self):

layer, _ = self._assert_basic_layer_properties(
self._image_layer_combo.value, ["Image"]
Expand All @@ -1832,11 +1832,11 @@ def _run_image_equalization(self):
else:
mask_layer_data = None

perc_low, perc_high = self._equalization_percentiles_slider.value
perc_low, perc_high = self._enhancement_percentiles_slider.value

if self._local_global_equalization_checkbox.value:
if self._local_global_enhancement_checkbox.value:

func_name = "global_image_equalization"
func_name = "global_contrast_enhancement"

func_params = {
"perc_low": perc_low,
Expand All @@ -1845,16 +1845,16 @@ def _run_image_equalization(self):
}

start_time = time.time()
equalized_array = global_image_equalization(
enhanced_array = global_contrast_enhancement(
layer.data, mask=mask_layer_data, **func_params
)
napari.utils.notifications.show_info(
f"Global equalization took {time.time() - start_time} seconds"
f"Global contrast enhancement took {time.time() - start_time} seconds"
)

else:

func_name = "local_image_equalization"
func_name = "local_contrast_enhancement"

func_params = {
"perc_low": perc_low,
Expand All @@ -1864,17 +1864,17 @@ def _run_image_equalization(self):
}

start_time = time.time()
equalized_array = local_image_equalization(
enhanced_array = local_contrast_enhancement(
layer.data, mask=mask_layer_data, **func_params
)
napari.utils.notifications.show_info(
f"Local equalization took {time.time() - start_time} seconds"
f"Local contrast enhancement took {time.time() - start_time} seconds"
)

name = f"{layer.name}_{self._adjective_dict[func_name]}"

if self._overwrite_checkbox.value:
layer.data = equalized_array
layer.data = enhanced_array
layer.contrast_limits = (0, 1)
layer.name = name
else:
Expand All @@ -1883,7 +1883,7 @@ def _run_image_equalization(self):
)
image_properties["contrast_limits"] = (0, 1)
self._viewer.add_image(
equalized_array,
enhanced_array,
name=name,
**image_properties,
)
Expand All @@ -1902,7 +1902,7 @@ def _run_image_equalization(self):
"Image",
)
output_params_to_layer_names_and_types_dict = OrderedDict(
[("equalized_image", (name, "Image"))]
[("enhanced_image", (name, "Image"))]
)
self._recorder.record(
function_name=func_name,
Expand Down
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