def copyImages(configFile, destination, onlyImage=True, prefix=''):
#Copys all images in configFile to destination folder
#Original folder will be used as prefix
#set onlyImage to False to also copy _mod.tif and dots.csv files
if not os.path.isdir(destination):
os.mkdir(destination)
config = file_utils.file2dict(configFile, ',\t')
folder = os.path.split(configFile)[0]
originImages = [
x + '.tif' for x in config['ROUTE'] if not x.endswith('_dupl')
]
destinationImages = [
prefix + x.replace('/', '__') for x in originImages
] #Subfolders names are used as prefix seperated by __
_copyFilesFromList(folder, originImages, destination, destinationImages)
if not onlyImage:
originMod = [
x + '_mod.tif' for x in config['ROUTE']
if os.path.isfile(os.path.join(folder, x) + '_mod.tif')
]
originDots = [
x + 'dots.csv' for x in config['ROUTE']
if os.path.isfile(os.path.join(folder, x) + 'dots.csv')
]
destinationMod = [prefix + x.replace('/', '__') for x in originMod]
destinationDots = [prefix + x.replace('/', '__') for x in originMod]
_copyFilesFromList(folder, originMod, destination, destinationMod)
_copyFilesFromList(folder, originDots, destination, destinationDots)
def copyTestImages(all_configs, sourcefolder, destinationfolder, modsuffix=''):
#Get the names of individual image files
imgFiles = file_utils.file2dict(all_configs, ';')['Name']
for f in imgFiles:
iPath = os.path.join(os.path.split(all_configs)[0], f[0:-3] + 'csv')
images = file_utils.file2dict(iPath, ';')
imgs = images['OriginalRoute']
types = images['Type']
imgs = [i for i, t in zip(imgs, types) if t == 'test']
sc = [os.path.join(sourcefolder, i) for i in imgs]
dst = [
os.path.join(destinationfolder,
os.path.split(i)[1]) for i in imgs
]
for s, d in zip(sc, dst):
copyfile(s + '.tif', d + '.tif')
copyfile(s + '_mod.tif', d + '_mod' + modsuffix + '.tif')
def getCoordinatesFromConfig(configFile,
outputPath=False,
downscale_factor=False):
config = file_utils.file2dict(configFile, ',\t')
folder = os.path.split(configFile)[0]
images = [os.path.join(folder, x) + '_mod.tif' for x in config['ROUTE']]
return getCoordinatesFromFiles(images, outputPath, downscale_factor)
def duplicateImage(configFile, index, copyMod=False, duplicate_suffix='_dupl'):
'''Duplicates image with index and adds duplicate to Darea project'''
#index starts from 0
images = file_utils.file2dict(configFile, ',\t')
imbasepath = os.path.join(os.path.dirname(configFile),
images['ROUTE'][index])
if 'ANGLES' in images and images['SELECTED'] != 'NaN':
isSerEM = True
else:
isSerEM = False
modbasepath = imbasepath
while imbasepath.endswith('_dupl'):
imbasepath = imbasepath[:-5]
impath = imbasepath if isSerEM else imbasepath + '.tif'
assert os.path.isfile(impath)
#Find a path to copy the image to, by appending duplicat_suffix until it is not already taken
cppath = imbasepath + duplicate_suffix
while os.path.relpath(cppath,
os.path.dirname(configFile)) in images['ROUTE']:
cppath += duplicate_suffix
cproute = os.path.relpath(
cppath, os.path.dirname(configFile)) #Will be written to config
cproute = cproute.replace('\\', '/') #Deal with windows issues
if copyMod and os.path.isfile(modbasepath + '_mod.tif'):
#Also duplicate _mod image if wanted and exists.
copyfile(modbasepath + '_mod.tif', cppath + '_mod.tif')
if copyMod and isSerEM:
i = 1
while os.path.isfile(f'{modbasepath}_mod_{i}.tif'):
copyfile(f'{modbasepath}_mod_{i}.tif', f'{cppath}_mod_{i}.tif')
i += 1
if copyMod and os.path.isfile(modbasepath + 'dots.csv'):
#Also duplicate dots file
copyfile(modbasepath + 'dots.csv', cppath + 'dots.csv')
if copyMod and isSerEM:
i = 1
while os.path.isfile(f'{modbasepath}dots_{i}.csv'):
copyfile(f'{modbasepath}dots_{i}.csv', f'{cppath}dots_{i}.csv')
i += 1
#copyfile(impath,cppath+'.tif') #don't copy image to save space
for k in images:
lst = images[k][0:index + 1]
if k == 'ROUTE':
lst.append(cproute)
else:
lst.append(images[k][index])
lst += images[k][index + 1:]
images[k] = lst
file_utils.dict2file(configFile, images, ',\t')
def removeImage(configFile, index):
'''Removes image with index from Darea project'''
#index starts from 0
if type(index) == int:
index = [index]
elif type(index) == list:
index.sort(reverse=True)
else:
print(
'Index needs to be an integer or a list of integers. Got {} with type {}'
.format(index, type(index)))
return
images = file_utils.file2dict(configFile, ',\t')
for idx in index:
for i in images:
del (images[i][idx])
file_utils.dict2file(configFile, images, ',\t')
def addImages(configFile, imagepaths, actualConfig=False):
#configFile is the one modified, but if actualConfig is provided,
#Relative path is taken from actualConfig
print(configFile)
print(imagepaths)
print(actualConfig)
images = file_utils.file2dict(configFile, ',\t')
imagepaths = [os.path.splitext(i)[0] for i in imagepaths]
for i in imagepaths:
print(i)
if actualConfig:
common_pref = os.path.commonprefix([i, actualConfig])
im = os.path.relpath(i, common_pref)
else:
common_pref = os.path.commonprefix([i, configFile])
im = os.path.relpath(i, common_pref)
print(im)
if im not in images['ROUTE']:
images['ROUTE'].append(im)
images['PIXELSIZE'].append('NaN')
images['GROUP'].append(os.path.split(im)[0])
file_utils.dict2file(configFile, images, ',\t')
def copyImagesfromChooser(destination,
choiceFile,
choicesToCopy,
keepStructure=False,
file_ext='.tif'):
''' Copys files chosen with matlab filechooser to destination folder
destination: destination Folder
choiceFile: Path to choice file made with matlab gpdq filechooser
choicesToCopy: List of strings specifying the choices which images should be copied
keepStructure: keeps Original folder structure. If False, will modify file names, numbering then will be 1.tif, 2.tif ...; If numbered files already at destination,
will increment numbers rather than overwriting files
file_ext: fileextenstion of images (in choice file, no fileextensions are saved) '''
file_utils.safe_mkdir(destination)
choices = file_utils.file2dict(choiceFile, delimiter='\t')
filesToCopy = [
f + file_ext for i, f in enumerate(choices['Image'])
if choices['Choice'][i] in choicesToCopy
]
print(filesToCopy)
if not filesToCopy:
return
if keepStructure:
#Needs to be implemented Still
pass
else:
nr_start = 1 + getMaxIntFromNumberedFiles(destination, file_ext)
fileDests = [
os.path.join(destination,
str(nr_start + i) + file_ext)
for i, _ in enumerate(filesToCopy)
]
for x, y in zip(filesToCopy, fileDests):
shutil.copyfile(x, y)
def changeSelectedAngle(configFile, index, newValue):
images = file_utils.file2dict(configFile, ',\t')
images['SELECTED'][index] = str(newValue)
file_utils.dict2file(configFile, images, ',\t')
def changeScales(configFile, indeces, newValues):
images = file_utils.file2dict(configFile, ',\t')
for index, newValue in zip(indeces, newValues):
images['PIXELSIZE'][index] = str(newValue)
file_utils.dict2file(configFile, images, ',\t')
def compareDemVis(configFile,
prediction_folder,
line,
plot=True,
cropsize=768):
config = file_utils.file2dict(configFile, ',\t')
folder = os.path.split(configFile)[0]
images = [os.path.join(folder, x) + '.tif' for x in config['ROUTE']]
image = [f for f in images if f.endswith(line[0] + '.tif')][0]
modImage = image[:-4] + '_mod.tif'
prediction = os.path.join(prediction_folder, os.path.split(image)[1])
img = cv2.cvtColor(cv2.imread(image), cv2.COLOR_RGB2GRAY)
if os.path.isfile(modImage):
modImg = cv2.cvtColor(cv2.imread(modImage), cv2.COLOR_RGB2GRAY)
else:
modImg = np.ones(img.shape, dtype=np.uint8) * np.iinfo(np.uint8).max
if os.path.isfile(modImage[0:-4] + '_morph.tif'):
morphModImg = invertImage(
cv2.cvtColor(cv2.imread(modImage[0:-4] + '_morph.tif'),
cv2.COLOR_RGB2GRAY))
else:
morphModImg = None
pred = invertImage(cv2.cvtColor(cv2.imread(prediction),
cv2.COLOR_RGB2GRAY))
if os.path.isfile(prediction[0:-4] + '_morph.tif'):
morphPred = invertImage(
cv2.cvtColor(cv2.imread(prediction[0:-4] + '_morph.tif'),
cv2.COLOR_RGB2GRAY))
else:
morphPred = None
if pred.shape != img.shape:
#Upscale prediction
pred = cv2.resize(pred, img.shape, cv2.INTER_NEAREST)
if morphPred is not None:
morphPred = cv2.resize(morphPred, img.shape, cv2.INTER_NEAREST)
try:
cropY1 = max(0, round(line[1][0] - cropsize / 2))
cropY2 = min(img.shape[1], round(line[1][0] + cropsize / 2))
cropX1 = max(0, round(line[1][1] - cropsize / 2))
cropX2 = min(img.shape[0], round(line[1][1] + cropsize / 2))
except:
print(line)
raise
plotted_images = [
img[cropX1:cropX2, cropY1:cropY2], modImg[cropX1:cropX2, cropY1:cropY2]
]
if morphModImg is not None:
plotted_images.append(morphModImg[cropX1:cropX2, cropY1:cropY2])
else:
plotted_images.append(None)
plotted_images.append(pred[cropX1:cropX2, cropY1:cropY2])
if morphPred is not None:
plotted_images.append(morphPred[cropX1:cropX2, cropY1:cropY2])
else:
plotted_images.append(None)
if not plot:
return plotted_images
plt.figure()
plt.imshow(plotted_images[0], cmap='gray')
for i, x in enumerate(plotted_images):
if x is None:
continue
plt.figure()
plt.imshow(x, cmap='gray', vmin=0, vmax=255)