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changes to step3 indexing #30

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Jul 3, 2024
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changes to step3 indexing #30

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116 changes: 65 additions & 51 deletions step3.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,13 +17,13 @@

# Define thresholds and parameters
pos = 'Pos0_2'
path = f'/Users/samarth/Documents/MATLAB/Full_Life_Cycle_tracking/{pos}/'
sav_path = '/Users/samarth/Documents/MATLAB/Full_Life_Cycle_tracking/saved_res/py_res'
path = f'/Users/samarth/Documents/MATLAB/Full_Life_Cycle_tracking/Python_Track_Test/Pro/'
sav_path = '/Users/samarth/Documents/MATLAB/Full_Life_Cycle_tracking/saved_res/py_res/'
shock_period = [122, 134]

# Load image file names
file_names = [f for f in os.listdir(path) if f.endswith('_Ph3_000_MAT16_18_masks.tif')]
file_numbers = [int(f.split('img_')[1].split('_Ph3_000_MAT16_18_masks.tif')[0]) for f in file_names]
file_names = [f for f in os.listdir(path) if f.endswith('_Ph3_000_cp_masks.tif')]
file_numbers = [int(f.split('img_')[1].split('_Ph3_000_cp_masks.tif')[0]) for f in file_names]

sorted_indices = np.argsort(file_numbers)
sorted_numbers = np.array(file_numbers)[sorted_indices]
Expand All @@ -40,12 +40,12 @@

# Remove shock-induced timepoints
mat_masks_original = mat_masks.copy()
for start, end in [shock_period]:
for i in range(start, end + 1):
mat_masks[i] = None
# for start, end in [shock_period]:
# for i in range(start, end + 1):
# mat_masks[i] = None

start = 0
for its in range(len(mat_masks)):
for its in range(1, len(mat_masks) + 1):
if mat_masks[its] is not None and np.sum(mat_masks[its]) > 0:
start = its
break
Expand All @@ -69,6 +69,13 @@
rang2 = rang
ccel = 1

# uq = mat_masks[50]
# print(np.unique(uq)[0:])
# plt.figure()
# plt.imshow(np.uint16(uq), cmap='gray')
# plt.title('uq')
# plt.show()

while xx != 0:
for im_no in rang2:
#I2 = mat_masks[im_no] if ccel == 1 else MATC[1][im_no]
Expand All @@ -81,53 +88,48 @@
continue


# =============================================================================
# plt.figure()
# plt.imshow(np.uint16(I2), cmap='gray')
# plt.title('I2')
# plt.show()
# =============================================================================
# plt.figure()
# plt.imshow(np.uint16(I2), cmap='gray')
# plt.title('I2')
# plt.show()

if(im_no < 280):
print(im_no, min(rang2))
# if(im_no < 280):
# print(im_no, min(rang2))

if im_no == min(rang2):
#TODO!
ind1 = np.unique(I2)[1:] # Exclude background
I3 = I2 == ind1[0]
I3 = (I2 == ind1[0])
I3A = I3
# plt.figure()
# plt.imshow(np.uint16(I3A), cmap='gray')
# plt.title('I3A')
# plt.show()
else:
I3A = IS6
# =============================================================================
# plt.figure()
# plt.imshow(np.uint16(I3A), cmap='gray')
# plt.title('I3A')
# plt.show()
# =============================================================================
# plt.figure()
# plt.imshow(np.uint16(I3A), cmap='gray')
# plt.title('I3A')
# plt.show()



I3A = skeletonize(I3A)
I2A = I2
I2A = np.copy(I2)
I3B = np.uint16(I3A) * np.uint16(I2A)

"""
plt.figure()
plt.imshow(np.uint16(I3A), cmap='gray')
plt.title('I3A')
plt.show()
"""

# plt.figure()
# plt.imshow(np.uint16(I3B), cmap='gray')
# plt.title('I3B')
# plt.imshow(np.uint16(I3A), cmap='gray')
# plt.title('I3A')
# plt.show()

"""

plt.figure()
plt.imshow(np.uint16(I3B), cmap='gray')
plt.title('I3B')
plt.show()
"""


ind = mode(I3B[I3B != 0])[0]

Expand All @@ -148,9 +150,9 @@
continue
elif ind == 0 and ccel != 1:
continue

pix = np.where(np.uint16(I2A == ind))
pix0 = np.where(np.uint16(I2A != ind))
pix = (I2A == ind)
pix0 = (I2A != ind)

I2A[pix] = ccel
I2A[pix0] = 0
Expand All @@ -164,14 +166,16 @@
"""

I22 = np.zeros_like(I2)
pix1 = np.where(IS6 == ccel)
pix1 = (IS6 == ccel)
I2[pix1] = 0

#TODO!
pix2 = np.unique(I2)[1:] # Exclude background

if ccel == 1:
for ity in pix2:
pix4 = np.where(I2 == ity)
I22[pix4] = ity
for ity in range(len(pix2)):
pix4 = np.where(I2 == pix2[ity])
I22[pix4] = ity + 1
MATC[0][im_no] = IS6
else:
if pix2.size > 0:
Expand All @@ -184,14 +188,14 @@
IS61[pix] = ccel
MATC[0][im_no] = np.uint16(IS61)

MATC[1][im_no] = I22
MATC[1][im_no] = I22.astype(np.uint16)


# plt.figure()
# plt.imshow(np.uint16(IS6), cmap='gray')
# plt.title('IS6')
# plt.show()

"""
plt.figure()
plt.imshow(np.uint16(IS6), cmap='gray')
plt.title('IS6')
plt.show()
"""

xx = 0
for i in rang:
Expand All @@ -204,6 +208,16 @@

ccel -= 1 # number of cells tracked

# for x in rang2:
# tracked = MATC[1][x]
# plt.figure()
# plt.imshow(np.uint16(tracked) == 1, cmap='gray')
# plt.title('tracked')
# plt.show()




# Removing the shock-induced points from rang
rang3 = list(rang)
for start, end in [shock_period]:
Expand Down Expand Up @@ -293,13 +307,13 @@ def replace_none_with_empty_array(data):
Matmasks = replace_none_with_empty_array(Matmasks)
mat_masks_original = replace_none_with_empty_array(mat_masks_original)
# Save results
sio.savemat(f'{sav_path}{pos}_MAT_16_18_Track.mat', {
sio.savemat(f'{sav_path}{pos}_sam_MAT_16_18_Track.mat', {
"Matmasks": Matmasks,
"no_obj": no_obj,
"all_obj": all_obj,
##"all_obj": all_obj,
"cell_data": cell_data,
"rang": rang,
"rang3": rang3,
##"rang3": rang3,
"shock_period": shock_period,
"mat_masks_original": mat_masks_original,
"start": start
Expand Down
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