def main(opts):
out = [opts['-o'],]
args = izip(ts_iter_images(opts['-i']), cycle(out))
count = 0
for _ in imap(process_image, args):
if count % 10 == 0:
print("Renamed {} images!".format(count), end="\r")
count += 1
print("Renamed {} images!\n\n".format(count))
def ts_to_tsnc(ts_path, tsnc_path):
log = logging.getLogger("timestreamlib")
# Get timestream images
imgs = list(ts_iter_images(ts_path))
# Make netcdf4 file
root = ncdf.Dataset(tsnc_path, 'w', format="NETCDF4")
root.createGroup('timestream')
# Make dimensions
# Kludge time!!!
root.createDimension('y', mat0.shape[0])
root.createDimension('x', mat0.shape[1])
root.createDimension('z', mat0.shape[2])
root.createDimension('t', None)
mat0 = None
mat_n = 0
while mat0 is None:
try:
mat0 = read_image(imgs[mat_n])
mat_n += 1
except IndexError:
raise ValueError("Didn't find a valid image in {}".format(ts_path))
# setup variables
times = root.createVariable("time", 'f8', ('t',))
times.units = "seconds since 1970-01-01 00:00:00.0"
times.calendar = "standard"
root.createVariable("z", 'u1', ('z',))
root.createVariable("y", 'u4', ('y',))
root.createVariable("x", 'u4', ('x',))
# create actual pixel array
px_type = 'u{:d}'.format(mat0.dtype.itemsize)
pixels = root.createVariable("pixel", px_type, ('t', 'y', 'x', 'z'),
zlib=True)
log.info("Created netcdf4 file {} with pixel array dimensions {!r}".format(
tsnc_path, pixels.shape))
# iteratively add images
count = 0
for img_n, mat in enumerate(imap(read_image, imgs)):
img = imgs[img_n]
if mat is None:
continue
n_dates = len(root.dimensions['t'])
time = ts_parse_date_path(img)
times[n_dates] = date2num([time, ], units=times.units,
calendar=times.calendar)
pixels[n_dates, :, :, :] = mat
count += 1
log.debug("Processed {}. Matrix shape is {!r}".format(img,
pixels.shape))
log.log(NOEOL, "Processed {: 5d} images.\r".format(count))
log.info("Processed {: 5d} images. ts_to_tsnc finished!".format(count))
root.close()
def main(opts):
pool = mp.Pool()
if opts['-t']:
pool = mp.Pool(opts['-t'])
xy = tuple(map(int, opts['-s'].replace('x', ',').split(',')))
if len(xy) == 1:
xy = (xy[0], 0)
xy = [xy, ]
out = [opts['-o'],]
args = izip(ts_iter_images(opts['-i']), cycle(out), cycle(xy))
count = 0
print("Resizing {} to {}".format(opts['-i'], opts['-s']))
for _ in pool.imap(process_image, args):
print("Resized {: 5d} images!".format(count), end="\r")
count += 1
print("Resized {: 5d} images! Done!".format(count))
pool.close()
pool.join()
def ts_to_tsnc(ts_path, tsnc_path):
log = logging.getLogger("CONSOLE")
# Get timestream images
imgs = list(ts_iter_images(ts_path))
mats = ts_iter_numpy(imgs)
# Make netcdf4 file
root = ncdf.Dataset(tsnc_path, 'w', format="NETCDF4")
root.createGroup('timestream')
# Make dimensions
# Kludge time!!!
mat0 = next(ts_iter_numpy([imgs[0], ]))[1]
root.createDimension('y', mat0.shape[0])
root.createDimension('x', mat0.shape[1])
root.createDimension('z', mat0.shape[2])
root.createDimension('t', None)
# setup variables
times = root.createVariable("time", 'f8', ('t',))
times.units = "seconds since 1970-01-01 00:00:00.0"
times.calendar = "standard"
root.createVariable("z", 'u1', ('z',))
root.createVariable("y", 'u4', ('y',))
root.createVariable("x", 'u4', ('x',))
# create actual pixel array
px_type = 'u{d}'.format(mat0.dtype.itemsize)
pixels = root.createVariable("pixel", px_type, ('t', 'y', 'x', 'z'),
zlib=True)
log.info("Created netcdf4 file {} with pixel array dimensions {!r}".format(
tsnc_path, pixels.shape))
# iteratively add images
count = 0
for img, mat in mats:
n_dates = len(root.dimensions['t'])
time = ts_parse_date_path(img)
times[n_dates] = date2num([time, ], units=times.units,
calendar=times.calendar)
pixels[n_dates, :, :, :] = mat
count += 1
log.debug("Processed {}. Matrix shape is {!r}".format(img,
pixels.shape))
if count % 2 == 0:
log.log(NOEOL, "Processed {: 5d} images.\r".format(count))
log.info("Processed {: 5d} images. ts_to_tsnc finished!".format(count))
root.close()
def test_good_timestream_manifold(self):
"""Test ts_iter_images with a timestream with a manifold"""
res = ts_iter_images(helpers.FILES["timestream_manifold"])
self.assertTrue(isgenerator(res))
self.assertListEqual(sorted(list(res)), helpers.TS_MANIFOLD_FILES_JPG)
def __init__(self, rootPath):
self.img_iter = ts_iter_images(rootPath)
self.counter = -1
def main(argv):
HelpString = 'correctDistortionAndColor.py -i <image file> ' + \
'-f <root image folder> '+ \
'-o <output file>\n' + \
'Example:\n' + \
"$ ./correctDistortionAndColor.py -f /mnt/phenocam/a_data/TimeStreams/BorevitzTest/BVZ0018/BVZ0018-GC04L~fullres-orig/ -k /mnt/phenocam/a_data/TimeStreams/BorevitzTest/BVZ0018/BVZ0018-GC04L~fullres-corr/calib_param_700Dcam.yml -g /mnt/phenocam/a_data/TimeStreams/BorevitzTest/BVZ0018/BVZ0018-GC04L~fullres-corr/CameraTrax_24ColorCard_2x3in.png -c /mnt/phenocam/a_data/TimeStreams/BorevitzTest/BVZ0018/BVZ0018-GC04L~fullres-corr/CameraTrax_24ColorCard_2x3inCaptured.png -o /mnt/phenocam/a_data/TimeStreams/BorevitzTest/BVZ0018/BVZ0018-GC04L~fullres-corr/ -j 16"
try:
opts, args = getopt.getopt(argv,"hi:f:c:k:b:g:t:o:j:",\
["ifile=","ifolder=","--configfolder","calibfile=","captured-colorcard=",\
"groundtruth-colorcard=","--tray-image-pattern","ofolder=","jobs="])
except getopt.GetoptError:
print(HelpString)
sys.exit(2)
if len(opts) == 0:
print(HelpString)
sys.exit()
ImageFile = ''
InputRootFolder = ''
OutputFolder = ''
InitialGeometryFile = 'ColorcardTrayPotSelections.yml'
ColorCardTrueFile = 'CameraTrax_24ColorCard_2x3in.png'
# ColorCardTrueFile = 'CameraTrax_24ColorCard_2x3in180deg.png'
# ColorCardCapturedFile = 'CameraTrax_24ColorCard_2x3inCaptured.png'
ColorCardCapturedFile = 'Card_%d.png'
TrayCapturedFile = 'Tray_%d.png'
PotCapturedFile = 'PotCaptured2.png' #'PotCaptured.png' #'PotCaptured4.png' #'PotCaptured3.png' #
CalibFile = 'Canon700D_18mm_CalibParam.yml'
ConfigFolder = ''
RotationAngle = None
NoJobs = 1
for opt, arg in opts:
if opt == '-h':
print(HelpString)
sys.exit()
elif opt in ("-i", "--ifile"):
ImageFile = arg
elif opt in ("-f", "--ifolder"):
InputRootFolder = arg
elif opt in ("-c", "--configfolder"):
ConfigFolder = arg
elif opt in ("-b", "--captured-colorcard"):
ColorCardCapturedFile = arg
elif opt in ("-g", "--groundtruth-colorcard"):
ColorCardTrueFile = arg
elif opt in ("-t", "--tray-image-pattern"):
TrayCapturedFile = arg
elif opt in ("-k", "--calibfile"):
CalibFile = arg
elif opt in ("-o", "--ofolder"):
OutputFolder = arg
elif opt in ("-j", "--jobs"):
NoJobs = int(arg)
if len(ConfigFolder) > 0:
ColorCardTrueFile = os.path.join(ConfigFolder, os.path.basename(ColorCardTrueFile))
ColorCardCapturedFile = os.path.join(ConfigFolder, os.path.basename(ColorCardCapturedFile))
TrayCapturedFile = os.path.join(ConfigFolder, os.path.basename(TrayCapturedFile))
PotCapturedFile = os.path.join(ConfigFolder, os.path.basename(PotCapturedFile))
CalibFile = os.path.join(ConfigFolder, os.path.basename(CalibFile))
InitialGeometryFile = os.path.join(ConfigFolder, os.path.basename(InitialGeometryFile))
if len(OutputFolder) > 0 and not os.path.exists(OutputFolder):
os.makedirs(OutputFolder)
if len(CalibFile) > 0:
ImageSize, SquareSize, CameraMatrix, DistCoefs, RVecs, TVecs = utils.readCalibration(CalibFile)
print('CameraMatrix =', CameraMatrix)
print('DistCoefs =', DistCoefs)
UndistMapX, UndistMapY = cv2.initUndistortRectifyMap(CameraMatrix, DistCoefs, \
None, CameraMatrix, ImageSize, cv2.CV_32FC1)
if len(InitialGeometryFile):
rotationAngle, distortionCorrected, colorcardList, trayList, potList = utils.readGeometries(InitialGeometryFile)
print('trayList =', trayList)
RotationAngle = rotationAngle
colorcardCentre, colorcardWidth, colorcardHeight, colorcardAngle = utils.getRectangleParamters(colorcardList[0])
colorcardPosition = [int(colorcardCentre[0]), int(colorcardCentre[1])]
print('colorcardPosition =', colorcardPosition)
potCentre, potWidth, potHeight, potAngle = utils.getRectangleParamters(potList[0])
potSize = (int(potWidth), int(potHeight))
print('potSize =', potSize)
trayPositions = []
for tray in trayList:
trayCentre, trayWidth, trayHeight, trayAngle = utils.getRectangleParamters(tray)
trayPositions.append([int(trayCentre[0]), int(trayCentre[1])])
P24ColorCardTrueImage = cv2.imread(ColorCardTrueFile)[:,:,::-1] # read and convert to R-G-B image
SquareSize = int(P24ColorCardTrueImage.shape[0]/4)
HalfSquareSize = int(SquareSize/2)
P24ColorCardCapturedImage = cv2.imread(ColorCardCapturedFile %0)[:,:,::-1] # read and convert to R-G-B image
P24ColorCardCaptured_PyramidImages = utils.createImagePyramid(P24ColorCardCapturedImage)
Tray_PyramidImagesList = []
for i in range(8):
TrayFilename = TrayCapturedFile %(i)
TrayImage = cv2.imread(TrayFilename)
if TrayImage == None:
print('Unable to read', TrayFilename)
# Tray_PyramidImages = None
continue
else:
TrayImage = TrayImage[:,:,::-1]
Tray_PyramidImages = utils.createImagePyramid(TrayImage)
Tray_PyramidImagesList.append(Tray_PyramidImages)
PotCapturedImage = cv2.imread(PotCapturedFile)[:,:,::-1] # read and convert to R-G-B image
# supress green channel
PotCapturedImage[:,:,1] = 0
if PotCapturedImage == None:
print('Unable to read', TrayFilename)
scaleFactor = potSize[1]/PotCapturedImage.shape[0]
print('scaleFactor', scaleFactor)
PotCapturedImage = cv2.resize(PotCapturedImage, potSize, interpolation = cv2.INTER_CUBIC)
print('PotCapturedImage.shape')
Pot_PyramidImages = utils.createImagePyramid(PotCapturedImage)
# collect 24 colours from the captured color card:
Colors = np.zeros([3,24])
for i in range(24):
Row = int(i/6)
Col = i - Row*6
rr = Row*SquareSize + HalfSquareSize
cc = Col*SquareSize + HalfSquareSize
Colors[0,i] = P24ColorCardTrueImage[rr,cc,0]
Colors[1,i] = P24ColorCardTrueImage[rr,cc,1]
Colors[2,i] = P24ColorCardTrueImage[rr,cc,2]
print('Colors = \n', Colors)
if len(ImageFile):
img_iter = [sorted(glob.glob(ImageFile))]
elif len(InputRootFolder):
img_iter = ts_iter_images(InputRootFolder)
else:
print('Need imput image for image folder')
return
ArgList = []
for i,ImageFile_ in enumerate(img_iter):
if i <= 830:
continue
if len(OutputFolder) > 0 and len(InputRootFolder) == 0:
OutputFile = os.path.join(OutputFolder, os.path.basename(ImageFile_))
elif len(OutputFolder) > 0 and len(InputRootFolder) > 0:
ImagePath = os.path.dirname(ImageFile_)
ImageName = os.path.basename(ImageFile_)
OutputPath = os.path.join(OutputFolder, ImagePath[len(InputRootFolder):])
OutputFile = os.path.join(OutputPath, ImageName)
ArgList.append([ImageFile_, RotationAngle, UndistMapX, UndistMapY, P24ColorCardCaptured_PyramidImages, colorcardPosition, Colors, Tray_PyramidImagesList, trayPositions, Pot_PyramidImages, OutputFile])
# if i == 50:
# break
Process = Pool(processes = NoJobs)
import time
time1 = time.time()
Results = Process.map(correctDistortionAndColor, ArgList)
# for Arg in ArgList:
# correctDistortionAndColor(Arg)
time2 = time.time()
json.dump(Results, open(os.path.join(OutputFolder, 'Result.json')))
InfoFile = os.path.join(OutputFolder, 'ColorCorrectionInfo.txt')
with open(InfoFile, 'w') as myfile:
myfile.write('It took %0.3f seconds to process %d files using %d processes\n' % (time2-time1, len(Results), NoJobs))
myfile.write('ImageFileName; MatchingScore; ColorPosition-X(-1.0 for undetected colorbar); ColorbarPosition-Y(-1.0 for undetected colorbar); CorrectionError(-1.0 for undetected colorbar)\n')
print('Finished. Saved color correction info to', InfoFile)
RotationAngle = RectData['RotationAngle']
Rect = RectData['Colorbar'].tolist()
print('Rect =', Rect)
Centre, Width, Height, Angle = getRectangleParamters(Rect)
print(Centre, Width, Height, Angle)
ColCardMapX, ColCardMapY = createMap(Centre, Width, Height, Angle)
P24ColorCard = cv2.imread('/home/chuong/Data/ColorbarPositions/CameraTrax_24ColorCard_2x3in.png')[:,:,::-1] # read and convert to R-G-B image
SquareSize = int(P24ColorCard.shape[0]/4)
HalfSquareSize = int(SquareSize/2)
P24ColorCardCaptured = cv2.imread('/home/chuong/Data/ColorbarPositions/CameraTrax_24ColorCard_2x3inCaptured.png')[:,:,::-1] # read and convert to R-G-B image
SquareSizeCaptured = int(P24ColorCardCaptured.shape[0]/4)
HalfSquareSizeCaptured = int(SquareSizeCaptured/2)
img_iter = ts_iter_images('/home/chuong/Data/ColorbarPositions')
#img_iter = ts_iter_images('/home/chuong/Data/BVZ0012-GC02L-CN650D-Cam01')
for ImageFile in img_iter:
Image = cv2.imread(ImageFile)[:,:,::-1]
print(ImageFile)
if Image.shape[0] > Image.shape[1]:
RotationAngle = 90
Image = rotateImage(Image, RotationAngle)
# maxVal, maxLoc = findColorbarPyramid(Image, P24ColorCardCaptured)
maxVal, maxLoc, RotationAngle2 = findColorbarPyramid(Image, P24ColorCardCaptured, NoLevels = 5, FinalLevel = 3)
if maxVal == None:
continue
RotationAngle = RotationAngle + RotationAngle2
# if maxVal < maxVal180:
# RotationAngle = RotationAngle + 180
# maxVal, maxLoc, maxVal180, maxLoc180 = maxVal180, maxLoc180, maxVal, maxLoc
