def stack_to_tif(stack_path, compress=1, wipe=False):
"""
:param stack_path: string, full path of .stack file to be converted to .tif
:param compress: int, compression level to use for tif file
:param wipe: bool, if True stack file will be deleted after saving as tif
:return:
"""
from numpy import array_equal
from os import remove
from os.path import split, sep
from numpy import fromfile
import volTools as volt
from skimage.external import tifffile as tif
dims = volt.getStackDims(split(stack_path)[0] + sep)
im = fromfile(stack_path, dtype='int16')
im = im.reshape(dims[-1::-1])
tif_path = stack_path.split('.')[0] + '.tif'
tif.imsave(tif_path, im, compress=compress)
if wipe:
check_file = tif.imread(tif_path)
if array_equal(check_file, im):
print('Deleting {0}...'.format(stack_path))
remove(stack_path)
else:
print('{0} and {1} differ... something went wrong!'.format(stack_path, tif_path))
def stack_loader(stack_path):
import volTools as volt
from numpy import fromfile
from os.path import sep, split
dims = volt.getStackDims(split(stack_path)[0] + sep)
im = fromfile(stack_path, dtype='int16')
im = im.reshape(dims[-1::-1])
return im
def tToZStacks(inDir):
'''
tToZStacks(inDir):
Writes the tStacks in 'inDir' to zStacks in 'inDir\\zStacks'
'''
import sys, os
sys.path.insert(0, 'C:/Users/pujalaa/Documents/Code/Python/code/codeFromNV')
sys.path.insert(0, 'C:/Users/pujalaa/Documents/Code/Python/code/util')
import time
import numpy as np
import volTools
imgDir = inDir
# allFilesInDir = os.listdir(imgDir)
fileExt = '.stack'
fileStem = 'Plane'
#tStacks = np.sort(list(filter(lambda x: x.startswith(fileStem),\
# allFilesInDir)))
stackDims = volTools.getStackDims(imgDir)
nTimePts = volTools.getNumTimePoints(imgDir)
outDir = os.path.join(imgDir,'zStacks')
if os.path.isdir(outDir):
print(outDir, '\n ...already exists!')
else:
os.mkdir(outDir)
print('Writing files...')
startTime = time.time()
for stackNum in range(stackDims[2]):
print('Reading plane ' + str(stackNum+1) + '...')
fn = fileStem + '%0.2d' % (stackNum+1) + fileExt
fp = os.path.join(imgDir,fn)
blah = np.fromfile(fp,dtype = 'uint16')
blah = np.reshape(blah,(nTimePts,stackDims[1], stackDims[0]))
print('Writing plane ' + str(stackNum+1) + '...')
for timePt in range(nTimePts):
fn = 'TM' + '%0.05d' % timePt + '.bin'
fp = os.path.join(outDir,fn)
file = open(fp,'ab')
file.write(blah[timePt])
file.close()
print(int(time.time()-startTime)/60,'min')
def stack_to_tif(stack_path):
"""
:param stack_path: string, full path of .stack file to be converted to .tif
:return:
"""
from os.path import split, sep
from numpy import fromfile
import volTools as volt
from skimage.external import tifffile as tif
dims = volt.getStackDims(split(stack_path)[0] + sep)
im = fromfile(stack_path, dtype='int16')
im = im.reshape(dims[-1::-1])
tif_path = stack_path.split('.')[0] + '.tif'
tif.imsave(tif_path, im, compress=1)