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Clean up comments & add SaveExcel / Saenopy option
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@davidbhr
davidbhr committed Nov 27, 2024
1 parent c9c0a8e commit 344a441
Showing 1 changed file with 32 additions and 39 deletions.
71 changes: 32 additions & 39 deletions CompactionAnalyzer/CompactionFunctions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -260,7 +260,8 @@ def StuctureAnalysisMain(fiber_list,
manual_segmention = False , # segmentation of mask by manual clicking the cell outline
plotting = True , # creates and saves individual figures additionally to the excel files
dpi = 200 , # resolution of figures
SaveNumpy = False , # saves numpy arrays for later analysis - can create large data files
SaveNumpy = True , # saves numpy arrays for later analysis
SaveExcel = True , # saves Excel files for later analysis
norm1=1,norm2 = 99 , # contrast spreading for input images between norm1- and norm2-percentile; values below norm1-percentile are set to zero and
# values above norm2-percentile are set to 1
### use norm1= 0,norm2 = 100 if no contras enhancement desired
Expand All @@ -270,7 +271,13 @@ def StuctureAnalysisMain(fiber_list,
segmention_min_area = 1000, # small bjects below this px-area are removed during cell segmentation
load_segmentation = False, # if True enter the path of the segementation.npy - file in path_seg
path_seg = None, # to load a mask
ignore_cell_outline=False): # if True the cell area is not set to nan and orientation are calculted everywhere - still the cell center is calculated from segmention
ignore_cell_outline=False, # if True the cell area is not set to nan and orientation are calculted everywhere - still the cell center is calculated from segmention


mode_saenopy=False): # only used for the Saenopy Version to return data files directly after single run



"""
Main analysis
Expand Down Expand Up @@ -491,7 +498,8 @@ def StuctureAnalysisMain(fiber_list,
results_total['Orientation (weighted by intensity and coherency)'].append(cos_dev_total3)

excel_total = pd.DataFrame.from_dict(results_total)
excel_total.to_excel(os.path.join(out_list[n],"results_total.xlsx"))
if SaveExcel:
excel_total.to_excel(os.path.join(out_list[n],"results_total.xlsx"))


"""
Expand Down Expand Up @@ -546,14 +554,18 @@ def StuctureAnalysisMain(fiber_list,

# create excel sheet with results for angle analysis
excel_angles= pd.DataFrame.from_dict(results_angle)
excel_angles.to_excel(os.path.join(out_list[n],"results_angles.xlsx"))

if SaveExcel:
excel_angles.to_excel(os.path.join(out_list[n],"results_angles.xlsx"))


"""
Distance Evaluation
"""

# initialize result dictionary

# def distance_analysis(shells,shell_width,dist_surface,scale,angle_dev, ori, orientation_dev, weight_image,im_fiber_g):

# initialize result dictionary
results_distance = {'Shell_mid (px)': [], 'Shell_mid (µm)': [], 'Intensity (accumulated)': [],
'Intensity (individual)': [], 'Intensity Norm (individual)': [],
'Intensity Norm (accumulated)': [], 'Angle (accumulated)': [], 'Angle (individual)': [], 'Angle (individual-weightInt)': [],
Expand All @@ -565,7 +577,7 @@ def StuctureAnalysisMain(fiber_list,
'Angle disttocenter (accumulated)': [], 'Angle disttocenter (individual)': [],
'Orientation disttocenter (accumulated)': [], 'Orientation disttocenter (individual)': [],
'Angle disttocenter (individual)': []
}
}

mask_shells = {'Mask_shell': [], 'Mask_shell_center': [] }
# shell distances
Expand Down Expand Up @@ -598,7 +610,7 @@ def StuctureAnalysisMain(fiber_list,
results_distance['Orientation (individual-weightInt)'].append(np.nanmean(orientation_dev[mask_shell]*ori[mask_shell]*weight_image[mask_shell]/np.nanmean(ori[mask_shell]*weight_image[mask_shell]) ))


# mean intensity
# mean intensity
results_distance['Intensity (accumulated)'].append(np.nanmean(im_fiber_g[mask_shell_lower])) # accumulation of lower shells
results_distance['Intensity (individual)'].append(np.nanmean(im_fiber_g[mask_shell]) ) # exclusively in certain shell

Expand Down Expand Up @@ -632,7 +644,8 @@ def StuctureAnalysisMain(fiber_list,
results_distance['Intensity Norm disttocenter (accumulated)'].extend(list(norm_accum_int_c) )
# create excel sheet with results for angle analysis
excel_distance = pd.DataFrame.from_dict(results_distance)
excel_distance.to_excel(os.path.join(out_list[n],"results_distance.xlsx"))
if SaveExcel:
excel_distance.to_excel(os.path.join(out_list[n],"results_distance.xlsx"))



Expand Down Expand Up @@ -661,11 +674,11 @@ def StuctureAnalysisMain(fiber_list,
#np.save(os.path.join(numpy_out, "mask_surface_shells.npy"),mask_shells['Mask_shell'])
#np.save(os.path.join(numpy_out, "mask_spherical_shells.npy"),mask_shells['Mask_shell_center'])

# check the shapes --> everything is the same format
# print(segmention["mask"][edge:-edge,edge:-edge].shape)
# print(orientation_dev.shape)
# print(normalize(im_fiber_n[edge:-edge,edge:-edge]).shape)
# print(angle_no_reference.shape)
# check the shapes --> everything is the same format
# print(segmention["mask"][edge:-edge,edge:-edge].shape)
# print(orientation_dev.shape)
# print(normalize(im_fiber_n[edge:-edge,edge:-edge]).shape)
# print(angle_no_reference.shape)


"""
Expand All @@ -682,25 +695,7 @@ def StuctureAnalysisMain(fiber_list,
plot_angle_dev(angle_map = orientation_dev, vmin=-1,vmax=1,
vec0=min_evec[:,:,0] ,vec1=min_evec[:,:,1] ,coherency_map=ori,
path_png= os.path.join(figures,"Orientation.png"),label="Orientation",dpi=dpi,cmap="coolwarm")
# plot orientation and angle deviation maps together with orientation structure
# plot_angle_dev(angle_map = angle_dev, vmin=0,vmax=90,
# vec0=min_evec[:,:,0] ,vec1=min_evec[:,:,1] ,coherency_map=ori,
# path_png= os.path.join(figures,"Angle_deviation.png"),label="Angle Deviation",dpi=dpi,cmap="viridis_r")

# # do not show the weighted ones here, as only the mean has the same range again and here angles can be smaller/large
# plot_angle_dev(angle_map = angle_dev_weighted2,
# vec0=min_evec[:,:,0] ,vec1=min_evec[:,:,1] ,coherency_map=ori,
# path_png= os.path.join(figures,"Angle_deviation_weighted.png"),label="Angle Deviation",dpi=dpi,cmap="viridis_r")
# plot_angle_dev(angle_map = orientation_dev_weighted2 ,
# vec0=min_evec[:,:,0] ,vec1=min_evec[:,:,1] ,coherency_map=ori,
# path_png= os.path.join(figures,"Orientation_weighted.png"),label="Orientation",dpi=dpi,cmap="viridis")

# # pure coherency and pure orientation
# plot_coherency(ori,path_png= os.path.join(figures,"coherency_noquiver.png"),
# label="Coherency",vmin=0,vmax=1,cmap="turbo",dpi=dpi)
# plot_coherency(orientation_dev,
# path_png= os.path.join(figures,"Orientation_noquiver.png"),
# label="Orientation",vmin=-1,vmax=1,cmap="coolwarm",dpi=dpi)



if cell_list == None:
Expand All @@ -726,8 +721,6 @@ def StuctureAnalysisMain(fiber_list,
orientation_dev, cmap_angle="coolwarm",
path_png= os.path.join(figures,"Orientation_overlay.png"),
label="Orientation",dpi=dpi,
# ,cmap_cell="Greys_r",cmap_fiber="Greys_r", ### use default values here
# cmap_angle="viridis", alpha_ori =0.8, alpha_cell = 0.4, alpha_fiber = 0.4,
omin=-1, omax=1,scale=scale)

else:
Expand Down Expand Up @@ -771,7 +764,6 @@ def StuctureAnalysisMain(fiber_list,


plt.close("all")


# Polar plots
plot_polar(results_angle['Angles Plotting'], results_angle['Coherency (weighted by intensity)'],
Expand Down Expand Up @@ -807,7 +799,6 @@ def StuctureAnalysisMain(fiber_list,
path_png=os.path.join(figures,"fiber_structure.png"),dpi=dpi ,scale=scale)



plt.close("all")
### DISTANCE PLOTS
# plot shells - deactived as it consumes a lot of time
Expand All @@ -825,8 +816,10 @@ def StuctureAnalysisMain(fiber_list,
plot_cell(im_cell_n, path_png=os.path.join(figures,"cell-raw.png"), scale=scale, dpi=dpi)
plot_cell(normalize(im_fiber_n[edge:-edge,edge:-edge]), path_png=os.path.join(figures,"fiber-raw.png"), scale=scale, dpi=dpi)

plt.close("all")

plt.close("all")

if mode_saenopy == True: # only evaluates a single item at each call and returns the arrays
return excel_total, excel_angles, excel_distance
return


Expand Down

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