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"^6.8.0.2" qtawesome = "^1.2.1" jointforces = "^1.0.7" -compactionAnalyzer = "^1.0.3" +compactionAnalyzer = "^1.0.5" numba = "^0.60.0" appdirs = "^1.4.4" superqt = "^0.6.7" diff --git a/saenopy/gui/orientation/modules/Detection.py b/saenopy/gui/orientation/modules/Detection.py index 1e6477c..049851e 100644 --- a/saenopy/gui/orientation/modules/Detection.py +++ b/saenopy/gui/orientation/modules/Detection.py @@ -99,7 +99,7 @@ def process(self, result: ResultOrientation, orientation_parameters: Orientation shell_width /= result.pixel_size from CompactionAnalyzer.CompactionFunctions import StuctureAnalysisMain - StuctureAnalysisMain(fiber_list=[result.image_fiber], + angle_no_reference, orientation_dev, ori, min_evex, excel_total, excel_angles, excel_distance = StuctureAnalysisMain(fiber_list=[result.image_fiber], cell_list=[result.image_cell], out_list=[result.output[:-len(".saenopyOrientation")]], scale=result.pixel_size, @@ -115,9 +115,13 @@ def process(self, result: ResultOrientation, orientation_parameters: Orientation angle_sections=orientation_parameters["angle_sections"], shell_width=shell_width, SaveNumpy=True, + mode_saenopy=True, ) - result.orientation_map = np.load(Path(result.output).parent / Path(result.output).stem / "NumpyArrays" / "OrientationMap.npy") + result.orientation_map = orientation_dev#np.load(Path(result.output).parent / Path(result.output).stem / "NumpyArrays" / "OrientationMap.npy") + result.coherence_map = ori + result.angle_to_x_map = angle_no_reference + result.orientation_vectors = min_evex result.save() diff --git a/saenopy/gui/orientation/modules/result.py b/saenopy/gui/orientation/modules/result.py index 61159c7..c1055bf 100644 --- a/saenopy/gui/orientation/modules/result.py +++ b/saenopy/gui/orientation/modules/result.py @@ -44,7 +44,11 @@ class Segmentation(TypedDict): class ResultOrientation(Saveable): __save_parameters__ = ['image_cell', 'image_fiber', 'pixel_size', 'output', 'segmentation_parameters', 'orientation_parameters', - 'segmentation', 'orientation_map', + 'segmentation', + 'orientation_map', + 'coherence_map', + 'angle_to_x_map', + 'orientation_vectors', 'shape', '___save_name__', '___save_version__'] ___save_name__ = "ResultOrientation" @@ -61,6 +65,9 @@ class ResultOrientation(Saveable): segmentation: Segmentation = None orientation_map: np.ndarray = None + coherence_map: np.ndarray = None + angle_to_x_map: np.ndarray = None + orientation_vectors: np.ndarray = None state: bool = False @@ -120,20 +127,29 @@ def get_data_structure(self): "voxel_size": [self.pixel_size, self.pixel_size, 1], "time_delta": None, "channels": ["cells", "fibers"], - "fields": { - "deformation": { - "type": "vector", - "measure": "deformation", - "unit": "pixel", - "name": "displacements_measured", + "maps": { + "orientation_cell_center": { + "measure": "orientation", + "unit": "", + "name": "orientation_cell_center", + "colormap": "coolwarm", + "lim": [-1, 1], }, - "forces": { - "type": "vector", - "measure": "force", - "unit": "pixel", - "name": "force", - } - } + "orientation_x_axis": { + "measure": "angle", + "unit": "", + "name": "orientation_x_axis", + "colormap": "gist_rainbow", + "lim": [-90, 90], + }, + "coherence": { + "measure": "normalized_strength", + "unit": "", + "name": "orientation_x_axis", + "colormap": "turbo", + "lim": [0, 1], + }, + }, } def get_image_data(self, time_point, channel="default", use_reference=False): @@ -141,10 +157,21 @@ def get_image_data(self, time_point, channel="default", use_reference=False): im = self.get_image(0) else: im = self.get_image(1) + edge = self.orientation_parameters["edge"] + im = im[edge:-edge, edge:-edge] if len(im.shape) == 2: return im[:, :, None, None] return im[:, :, :, None] + def get_map_data(self, name): + if name == "orientation_cell_center": + return self.orientation_map + if name == "orientation_x_axis": + return self.angle_to_x_map + if name == "coherence": + return self.coherence_map + + def get_field_data(self, name, time_point): class Mesh2D: pass