def runTilePreproc(self, colObj):
if (type(self.runChannels) is not list):
self.runChannels = [self.runChannels]
for tileChanId in self.runChannels:
"""
ext, _ = colObj.getExtensionInfoById(tileChanId)
extSpl = ext.split('.')
extUse = extSpl[0] + str(self.channelToSave) + '.' + extSpl[1]
"""
for tile in colObj.dataListForRun:
path = os.path.join(self.getDirectoryPaths(colObj),
tile + '_' + self.ext)
code = util_functions.read_or_new_pickle(path)
if (code == 0):
im = colObj.loadTileDataByExtension(tile, tileChanId)
assert (len(im.shape) == 3)
imSplit = np.squeeze(im[:, :, self.channelToSave])
util_functions.read_or_new_pickle(path,
toSave=1,
variable_to_save=imSplit)
def runTilePreproc(self, colObj):
#for each tile, apply the operation (e.g., rescaling). Check whether this exists otherwise, call the tile operator
for tile in colObj.dataListForRun:
path = os.path.join(self.getDirectoryPaths(colObj),
tile + '_' + self.ext)
code = util_functions.read_or_new_pickle(path)
if (code == 0):
# get a list of all the tiles to operate on based on the specified channels to run on
tileData = []
for tileChanId in self.opChans:
try:
tileData.append(
colObj.loadTileDataByExtension(tile, tileChanId))
except IOError:
continue
if len(tileData) == 0:
continue
opTile = self.opDet.run(tileData)
util_functions.read_or_new_pickle(path,
toSave=1,
variable_to_save=opTile)
def runAction(self, colObj):
# function to extract the chips from the tiles
gridList = self.makeGrid(
[colObj.tileSize[0] + self.pad, colObj.tileSize[1] + self.pad])
directory = self.getDirectoryPaths(colObj)
# extract chips for all the specified extensions
# precompute extensions
fileExts = []
for cnt, chanId in enumerate(self.runChannels):
ext, _ = colObj.getExtensionInfoById(chanId)
if (self.saveExts is not None):
sExt = ext.split('.')
fileExts.append(sExt[0] + '.' + self.saveExts[cnt])
else:
fileExts.append(ext)
f_temp = []
for i in range(len(fileExts)):
f_temp.append([])
for ind, tilename in enumerate(tqdm(colObj.dataListForRun)):
if self.isTrain:
# check if gt exists for this tile
try:
colObj.loadTileDataByExtension(
tilename, self.runChannels[self.gtInd])
except IOError:
# skip this if there's not enough channels
continue
for cnt, (ext, chanId) in enumerate(zip(fileExts,
self.runChannels)):
cIm = colObj.loadTileDataByExtension(tilename, chanId)
if self.pad > 0:
cIm = np.pad(cIm,
((self.pad, self.pad), (self.pad, self.pad)),
'symmetric')
nDims = cIm.shape
for coordList in gridList:
# extract patches for all the channels at coordinate location.
# This is done so that the file containing patch names can have all
# the extracted patches of one location on a single line
x1 = int(coordList[0])
x2 = int(coordList[1])
finNm = tilename + '_y%dx%d_%s' % (x1, x2, ext)
fPath = os.path.join(directory, finNm)
isExt = util_functions.read_or_new_pickle(fPath, toLoad=0)
if (isExt == 0):
# extract a patch from the image
if (len(nDims) == 2):
chipDat = cIm[x1:x1 + self.chipExtrSize[0],
x2:x2 + self.chipExtrSize[1]]
else:
chipDat = cIm[x1:x1 + self.chipExtrSize[0],
x2:x2 + self.chipExtrSize[1], :]
util_functions.read_or_new_pickle(
fPath, toSave=1, variable_to_save=chipDat)
f_temp[cnt].append(finNm)
with open(os.path.join(directory, uabPatchExtrPurge.fname),
'w') as file:
for i in range(len(f_temp[0])):
s = []
for j in range(len(f_temp)):
s.append(f_temp[j][i])
file.write('{}\n'.format(' '.join(s)))
# make new dir
directory_new = uabBlock.getBlockDir(
os.path.join(uabBlockparent.outputDirs['patchExt'], colObj.colName,
self.algoName() + 'Purge'))
if not os.path.exists(directory_new):
os.makedirs(directory_new)
files = os.path.join(directory, 'fileList.txt')
with open(files, 'r') as f:
file_list = f.readlines()
file_list_new = []
for file in tqdm(file_list):
f_array = file.strip().split(' ')
rgb = []
for i in f_array[:3]:
rgb.append(imageio.imread(os.path.join(directory, i)))
rgb = np.dstack(rgb)
gt = imageio.imread(os.path.join(directory, f_array[-1]))
m_pcent, mask = compute_missing_percentage(rgb)
if m_pcent < 0.2:
file_list_new.append(file)
for i in f_array[:3]:
copyfile(os.path.join(directory, i),
os.path.join(directory_new, i))
if m_pcent > 0:
gt_new = (gt * mask).astype(np.uint8)
imageio.imsave(os.path.join(directory_new, f_array[-1]),
gt_new)
else:
copyfile(os.path.join(directory, f_array[-1]),
os.path.join(directory_new, f_array[-1]))
files = os.path.join(directory_new, 'fileList.txt')
with open(files, 'w+') as f:
for file in file_list_new:
f.write(file)
# remove old directory
rmtree(directory)
files = os.path.join(directory_new, 'state.txt')
with open(files, 'w+') as f:
f.write('Finished\n')
# rename directory
os.rename(directory_new, directory)
def runAction(self, colObj):
# function to extract the chips from the tiles
gridList = self.makeGrid(
[colObj.tileSize[0] + self.pad, colObj.tileSize[1] + self.pad],
self.numPerTile)
directory = self.getDirectoryPaths(colObj)
# extract chips for all the specified extensions
# precompute extensions
fileExts = []
for cnt, chanId in enumerate(self.runChannels):
ext, _ = colObj.getExtensionInfoById(chanId)
if (self.saveExts is not None):
sExt = ext.split('.')
fileExts.append(sExt[0] + '.' + self.saveExts[cnt])
else:
fileExts.append(ext)
f_temp = []
for i in range(len(fileExts)):
f_temp.append([])
for ind, tilename in enumerate(tqdm(colObj.dataListForRun)):
if self.isTrain:
# check if gt exists for this tile
try:
colObj.loadTileDataByExtension(
tilename, self.runChannels[self.gtInd])
except IOError:
# skip this if there's not enough channels
continue
for cnt, (ext, chanId) in enumerate(zip(fileExts,
self.runChannels)):
cIm = colObj.loadTileDataByExtension(tilename, chanId)
if self.pad > 0:
cIm = np.pad(cIm,
((self.pad, self.pad), (self.pad, self.pad)),
'symmetric')
nDims = cIm.shape
for coordList in gridList:
# extract patches for all the channels at coordinate location.
# This is done so that the file containing patch names can have all
# the extracted patches of one location on a single line
x1 = int(coordList[0])
x2 = int(coordList[1])
finNm = tilename + '_y%dx%d_%s' % (x1, x2, ext)
fPath = os.path.join(directory, finNm)
isExt = util_functions.read_or_new_pickle(fPath, toLoad=0)
if (isExt == 0):
# extract a patch from the image
if (len(nDims) == 2):
chipDat = cIm[x1:x1 + self.chipExtrSize[0],
x2:x2 + self.chipExtrSize[1]]
else:
chipDat = cIm[x1:x1 + self.chipExtrSize[0],
x2:x2 + self.chipExtrSize[1], :]
util_functions.read_or_new_pickle(
fPath, toSave=1, variable_to_save=chipDat)
f_temp[cnt].append(finNm)
with open(os.path.join(directory, uabPatchExtr.fname),
'w') as file:
for i in range(len(f_temp[0])):
s = []
for j in range(len(f_temp)):
s.append(f_temp[j][i])
file.write('{}\n'.format(' '.join(s)))