added evaluated measurement example load for spheroid

Author: rgerum

saenopy/examples.py

@@ -165,8 +165,8 @@ def get_examples_spheroid():
             "input": example_path / 'MCF7-time-lapse/20160912-122130_Mic3_rep?_pos*_x0_y0_modeBF_zMinProj.tif',
             "output_path": example_path / 'MCF7-time-lapse/example_output',
             "url": "https://github.com/rgerum/saenopy/releases/download/v0.7.4/MCF7-time-lapse.zip",
-            #"url_evaluated": "https://github.com/rgerum/saenopy/releases/download/v0.7.4/MCF7-time-lapse_evaluated.zip",
-            #"url_evaluated_file": ["KO/04_bf_before.saenopy2D", "KO/05_bf_before.saenopy2D", "WT/03_bf_before.saenopy2D", "WT/10_bf_before.saenopy2D"],
+            "url_evaluated": "https://github.com/rgerum/saenopy/releases/download/v0.7.4/MCF7-time-lapse_evaluated.zip",
+            "url_evaluated_file": ["20160912-122130_Mic3_rep{t}_pos6_x0_y0_modeBF_zMinProj.saenopySpheroid"],
         },
     }
 

saenopy/gui/common/AddFilesDialog.py

@@ -1,5 +1,6 @@
 import sys
 import os
+import time
 from qtpy import QtCore, QtWidgets, QtGui
 from saenopy.gui.common import QtShortCuts
 import saenopy
@@ -10,7 +11,7 @@ class AddFilesDialog(QtWidgets.QDialog):
     mode_data: str = None
     start_time: float = 0
 
-    file_extenstion = None
+    file_extension = None
     settings_group = "batch"
 
     examples_list = None
@@ -19,11 +20,11 @@ def add_new_measurement_tab(self):
         pass
 
     def add_existing_measurent_tab(self):
-        if self.file_extenstion is None:
+        if self.file_extension is None:
             return
         with self.tabs.createTab("Existing Measurement") as self.tab3:
             self.outputText3 = QtShortCuts.QInputFilename(None, "output", settings=self.settings,
-                                                          file_type=f"Results Files (*{self.file_extenstion})",
+                                                          file_type=f"Results Files (*{self.file_extension})",
                                                           settings_key=f"{self.settings_group}/wildcard_existing",
                                                           allow_edit=True, existing=True)
             self.tab3.addStretch()

saenopy/gui/solver/modules/load_measurement_dialog.py

@@ -1,23 +1,15 @@
-import sys
 from qtpy import QtCore, QtWidgets, QtGui
-import time
 
-import saenopy
-import saenopy.multigrid_helper
-import saenopy.get_deformations
-import saenopy.multigrid_helper
-import saenopy.materials
 from saenopy.gui.common import QtShortCuts
 from saenopy.gui.common.stack_selector import StackSelector
 from saenopy.gui.common.stack_selector_crop import StackSelectorCrop
 from saenopy.gui.common.stack_preview import StackPreview
-
 from saenopy.examples import get_examples
-
 from saenopy.gui.common.AddFilesDialog import AddFilesDialog
 
+
 class AddFilesDialog(AddFilesDialog):
-    file_extenstion = ".saenopy"
+    file_extension = ".saenopy"
     settings_group = "batch"
 
     examples_list = get_examples()

saenopy/gui/spheroid/modules/AddFilesDialog.py

@@ -1,39 +1,18 @@
-import sys
-
-# Setting the Qt bindings for QtPy
 import os
 
-import pandas as pd
-import qtawesome as qta
-
-os.environ["QT_API"] = "pyqt5"
-
 from qtpy import QtCore, QtWidgets, QtGui
 
 import numpy as np
 from natsort import natsorted
 
-
-from saenopy.gui.common import QtShortCuts, QExtendedGraphicsView
-from qimage2ndarray import array2qimage
-import matplotlib.pyplot as plt
-import imageio
-import threading
-import glob
-import time
-
-from matplotlib.figure import Figure
-import jointforces as jf
-import urllib
-from pathlib import Path
-
-import ctypes
-import saenopy
+from saenopy.gui.common import QtShortCuts
 from saenopy.examples import get_examples_spheroid
 from saenopy.gui.common.AddFilesDialog import AddFilesDialog
 
+
 class AddFilesDialog(AddFilesDialog):
     settings_group = "open_sheriod"
+    file_extension = ".saenopySpheroid"
 
     examples_list = get_examples_spheroid()
 

saenopy/gui/spheroid/modules/BatchEvaluate.py

@@ -70,6 +70,13 @@ def add_measurement(self):
             output_path = example["output_path"]
             pixel_size = example["pixel_size"]
             time_delta = example["time_delta"]
+        elif dialog.mode == "example_evaluated":
+            self.load_from_path(dialog.examples_output)
+            return
+        # load existing files
+        elif dialog.mode == "existing":
+            self.load_from_path(dialog.outputText3.value())
+            return
 
         results = get_stacks_spheroid(
             input_path,

saenopy/gui/spheroid/modules/result.py

@@ -65,7 +65,6 @@ def __init__(self, template, images, output, **kwargs):
         self.res_angles = {}
 
         super().__init__(**kwargs)
-        print(self.pixel_size)
 
     def save(self, file_name=None):
         if file_name is None:
@@ -100,14 +99,12 @@ def get_data_structure(self):
 
     def get_image_data(self, time_point, channel="default", use_reference=False):
         im = imread(self.images[time_point])
-        print(im.shape, im.dtype)
         if len(im.shape) == 2:
             return im[:, :, None, None]
         return im[:, :, :, None]
 
     def get_field_data(self, name, time_point):
         if self.displacements is not None and time_point > 0:
-            print(time_point)
             try:
                 disp = self.displacements[time_point - 1]
                 mesh = Mesh2D()
@@ -118,7 +115,6 @@ def get_field_data(self, name, time_point):
                 if mesh is not None:
                     return mesh, mesh.displacements_measured
             except IndexError:
-                print("index err")
                 pass
         return None, None
 
@@ -143,7 +139,6 @@ def get_stacks_spheroid(input_path, output_path,
                load_existing=False) -> List[ResultSpheroid]:
     text = os.path.normpath(input_path)
     glob_string = text.replace("?", "*")
-    # print("globbing", glob_string)
     files = natsorted(glob.glob(glob_string))
 
     output_base = glob_string
@@ -156,7 +151,6 @@ def get_stacks_spheroid(input_path, output_path,
     results = []
     for file in files:
         file = os.path.normpath(file)
-        #print(file, regex_string)
         match = re.match(regex_string, file).groups()
         reconstructed_file = regex_string
         for element in match:
@@ -165,7 +159,7 @@ def get_stacks_spheroid(input_path, output_path,
         reconstructed_file = re.sub(r'\\(.)', r'\1', reconstructed_file)
 
         if reconstructed_file not in data_dict:
-            output = Path(output_path) / os.path.relpath(file, output_base)
+            output = Path(output_path) / os.path.relpath(reconstructed_file.replace("*", "{t}"), output_base)
             output = output.parent / (output.stem + ".saenopySpheroid")
 
             if output.exists():

saenopy/gui/tfm2d/modules/CalculateDisplacements.py

@@ -13,7 +13,7 @@
 from pyTFM.TFM_functions import calculate_deformation
 from pyTFM.plotting import show_quiver
 from pyTFM.frame_shift_correction import correct_stage_drift
-from saenopy.gui.solver.modules.code_export import get_code
+from saenopy.gui.common.code_export import get_code
 from typing import List, Tuple
 
 

saenopy/gui/tfm2d/modules/CalculateForceGeneration.py

@@ -18,7 +18,7 @@
 except ImportError:
     from scipy.ndimage.morphology import binary_fill_holes
 from pyTFM.grid_setup_solids_py import interpolation  # a simple function to resize the mask
-from saenopy.gui.solver.modules.code_export import get_code
+from saenopy.gui.common.code_export import get_code
 from typing import List, Tuple
 
 

saenopy/gui/tfm2d/modules/CalculateForces.py

@@ -12,7 +12,7 @@
 from pyTFM.TFM_functions import TFM_tractions
 from pyTFM.plotting import show_quiver
 import numpy as np
-from saenopy.gui.solver.modules.code_export import get_code
+from saenopy.gui.common.code_export import get_code
 from typing import List, Tuple
 
 

saenopy/gui/tfm2d/modules/CalculateStress.py

@@ -25,7 +25,7 @@
 from pyTFM.plotting import plot_continuous_boundary_stresses
 from pyTFM.stress_functions import all_stress_measures, coefficient_of_variation
 from pyTFM.stress_functions import mean_stress_vector_norm
-from saenopy.gui.solver.modules.code_export import get_code
+from saenopy.gui.common.code_export import get_code
 from typing import List, Tuple
 
 

saenopy/gui/tfm2d/modules/DisplayCellImage.py

@@ -1,6 +1,6 @@
 from .PipelineModule import PipelineModule
 from tifffile import imread
-from saenopy.gui.solver.modules.code_export import get_code
+from saenopy.gui.common.code_export import get_code
 from typing import List, Tuple
 from saenopy.gui.tfm2d.modules.result import Result2D, get_stacks2D
 from pathlib import Path

saenopy/gui/tfm2d/modules/DisplayDeformed.py

@@ -6,7 +6,7 @@
 from pyTFM.frame_shift_correction import correct_stage_drift
 from .result import Result2D
 from pathlib import Path
-from saenopy.gui.solver.modules.code_export import get_code
+from saenopy.gui.common.code_export import get_code
 from typing import List, Tuple
 
 class DeformationDetector2(PipelineModule):

saenopy/gui/tfm2d/modules/load_measurement_dialog.py

@@ -18,7 +18,7 @@
 from saenopy.gui.common.AddFilesDialog import AddFilesDialog
 
 class AddFilesDialog(AddFilesDialog):
-    file_extenstion = ".saenopy2D"
+    file_extension = ".saenopy2D"
     settings_group = "open_2d"
 
     examples_list = get_examples_2D()