script for micheal

analysis_and_testing/micheal_analysis.py

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+from PIL import Image
+import numpy as np
+import os
+import matplotlib.pyplot as plt
+from pyTFM.frame_shift_correction import correct_stage_drift_stack
+from scipy.ndimage.interpolation import shift
+from pyTFM.TFM_functions import calculate_deformation, ffttc_traction
+from pyTFM.plotting import show_quiver
+from tqdm import tqdm
+
+# loading masks and images
+ims = Image.open("/home/andreas/Desktop/MichealTFM/ForceImage_TimeDependent.tif")
+images = []
+for i in range(ims.n_frames):
+    ims.seek(i)
+    images.append(np.array(ims))
+images = np.array(images)
+
+ms = Image.open("/home/andreas/Desktop/MichealTFM/Masks_TimeDependent.tif")
+masks = []
+for i in range(ms.n_frames):
+    ms.seek(i)
+    masks.append(np.array(ms))
+
+#ref = np.array(Image.open("/home/andreas/Desktop/MichealTFM/Null_SingleCell.tif"))
+# correting the stage drift
+
+# calculate drifts with respect to reference image
+ref = images[0] # reference doesnt look much like the images in the stack
+images, ref = correct_stage_drift_stack(images, ref)
+
+
+# deformation calculation
+deformations = []
+for i, im in tqdm(enumerate(images)):
+    defx, defy, _, _ = calculate_deformation(ref, im)
+    deformations.append((defx, defy))
+
+# tractions
+tractions = []
+for (defx, defy) in deformations:
+    tx, ty = ffttc_traction(defx, defy, pixelsize1=1, pixelsize2=2, young=1, sigma=0.5, filter="gaussian", fs=1)
+    tractions.append((tx, ty))
+
+
+# display of the fields
+plt.ioff() # turns off pop up plots
+folder = "/home/andreas/Desktop/MichealTFM/corrected"
+os.makedirs(folder, exist_ok=True)
+resolution = 200
+figsize = (ref.shape[1]/resolution, ref.shape[0]/resolution)
+cbar_style = "clickpoints"
+plot_style = "clickpoints"
+for i in range(len(images)):
+    Image.fromarray(images[i]).save(os.path.join(folder, "%03d.png" % i))
+    if i > 0:
+        fig, axis = show_quiver(deformations[i][0], deformations[i][1], cbar_str="deformations",
+                                figsize=figsize, resolution=resolution, cbar_style=cbar_style, plot_style=plot_style)
+        fig.savefig(os.path.join(folder, "def_%03d.png" % i ), facecolor=fig.get_facecolor(),
+                    edgecolor=fig.get_facecolor(), dpi=resolution)
+        fig, axis = show_quiver(tractions[i][0], tractions[i][1], cbar_str="tractions",
+                                figsize=figsize, resolution=resolution, cbar_style=cbar_style, plot_style=plot_style)
+        fig.savefig(os.path.join(folder, "tractions_%03d.png" % i ), facecolor=fig.get_facecolor(),
+                    edgecolor=fig.get_facecolor(), dpi=resolution)
+plt.ion()
+
+## make a clickpoints database
+import clickpoints
+db = clickpoints.DataFile(os.path.join(folder, "db.cdb"),"w")
+
+db.setLayer(layer_name="images")
+db.setLayer(layer_name="deformations")
+db.setLayer(layer_name="tractions")
+
+
+for im in os.listdir(folder):
+    if im.endswith(".png"):
+        frame = int(im[-7:-4])
+        layer = "images"
+        if "def" in im:
+            layer = "deformations"
+        if "tractions" in im:
+            layer = "tractions"
+        db.setImage(sort_index=frame, filename=os.path.join(folder, im), layer=layer)
+db.db.close()
+
+
+# analysis
+
+
+
+# traction and deformation analysis:
+