def compose_galleries(path, path_hmm, quality="90", one_daughter=True, sample=30):
logger = logging.getLogger('compose_galleries')
column_name = 'Trajectory'
path_index = os.path.join(path_hmm, '_index')
if not os.path.isdir(path_index):
logger.warning("Index path '%s' does not exist. Make sure the error correction was executed successfully." %
path_index)
return
for filename in os.listdir(path_index):
logger.info('Creating gallery overview for %s' % filename)
group_name = os.path.splitext(filename)[0]
t = read_table(os.path.join(path_index, filename))[1]
t.reverse()
if one_daughter:
for record in t[:]:
if record[column_name].split('__')[4] != 'B01':
t.remove(record)
n = len(t)
if not sample is None and sample <= n:
idx = random.sample(xrange(n), sample)
idx.sort()
d = [t[i] for i in idx]
else:
d = t
n = len(d)
results = {}
for idx, record in enumerate(d):
#print idx, record
traj = record[column_name]
items = traj.split('__')
pos = items[1][1:]
key = '__'.join(items[1:5])
gallery_path = os.path.join(path, 'analyzed', pos, 'gallery')
if os.path.isdir(gallery_path):
for gallery_name in os.listdir(gallery_path):
img = ccore.readImageRGB(os.path.join(gallery_path, gallery_name, '%s.jpg' % key))
if gallery_name not in results:
results[gallery_name] = ccore.RGBImage(img.width, img.height*n)
img_out = results[gallery_name]
ccore.copySubImage(img,
ccore.Diff2D(0, 0),
ccore.Diff2D(img.width, img.height),
img_out,
ccore.Diff2D(0, img.height*idx))
for gallery_name in results:
path_out = os.path.join(path_hmm, '_gallery', gallery_name)
safe_mkdirs(path_out)
image_name = os.path.join(path_out, '%s.jpg' % group_name)
ccore.writeImage(results[gallery_name], image_name, quality)
logger.debug("Gallery image '%s' successfully written." % image_name)
yield group_name
def getBackgroundForImage(self, imgIn, imgMask, outFilenameBase=None):
mask_histo = [
x * imgMask.width * imgMask.height
for x in imgMask.getHistogram(256)
]
area_objects = mask_histo[0]
area_background = sum(mask_histo[1:])
# pos, t, channel, path + filename
imgConv = ccore.conversionTo8Bit(imgIn, 2**15, 2**15 + 4096, 0, 255)
imgInf = ccore.infimum(imgMask, imgConv)
inf_histo = [
x * (imgInf.width * imgInf.height) / area_background
for x in imgInf.getHistogram(256)
]
if self.oSettings.write_images and not outFilenameBase is None:
outDir = os.path.dirname(outFilenameBase)
filename = os.path.basename(outFilenameBase)
if not os.path.isdir(outDir):
os.makedirs(outDir)
ccore.writeImage(
imgConv,
os.path.join(outDir,
'convert_%s' % filename.replace('tif', 'png')))
ccore.writeImage(
imgInf,
os.path.join(outDir,
'inf_%s' % filename.replace('tif', 'png')))
# we exclude the object pixels from the analysis
inf_histo[0] = 0
# get statistical values
meanval_background = sum([inf_histo[i] * i for i in range(256)])
sumval = 0.0
medianval_background = -1
quantile25 = -1
for i in range(256):
sumval += inf_histo[i]
if sumval >= 0.25 and quantile25 < 0:
quantile25 = i
if sumval >= 0.5 and medianval_background < 0:
medianval_background = i
break
res = {
'mean': meanval_background,
'median': medianval_background,
'25quantile': quantile25
}
return res
def convertToOneFilePerTrack(cls, path_out, image_compression=''):
for event_id in os.listdir(path_out):
event_path = os.path.join(path_out, event_id)
#print event_path
if os.path.isdir(event_path):
# get all image cutter files
filenames = collect_files(event_path,
extensions=['.jpg', '.png', '.tif'],
absolute=True)
if len(filenames) > 0:
img_out = None
# determine file extension
ext = os.path.splitext(filenames[0])[1]
# stitch image horizontally
for idx, filename in enumerate(filenames):
img = cls.read_image(filename)
if img_out is None:
size = img.width, img.height
img_out = cls.IMAGE_CLASS(size[0] * len(filenames),
size[1])
ccore.copySubImage(img,
ccore.Diff2D(0, 0),
ccore.Diff2D(size[0], size[1]),
img_out,
ccore.Diff2D(size[0]*idx, 0))
# save a one file with event_id (P,T,O) + extension
filename_out = os.path.join(path_out, event_id) + ext
#print filename_out
ccore.writeImage(img_out,
filename_out)
path_out_info = os.path.join(path_out, '_info')
makedirs(path_out_info)
shutil.copy2(os.path.join(event_path, '_%s.txt' % event_id),
os.path.join(path_out_info, '_%s.txt' % event_id))
shutil.rmtree(event_path, ignore_errors=True)
def render(self,
strPathOut,
dctRenderInfo=None,
strFileSuffix='.jpg',
strCompression='98',
writeToDisc=True,
images=None):
lstImages = []
if not images is None:
lstImages += images
if dctRenderInfo is None:
for name, oChannel in self._channel_registry.iteritems():
for strRegion, oContainer in oChannel.containers.iteritems():
strHexColor, fAlpha = oChannel.dctAreaRendering[strRegion]
imgRaw = oChannel.meta_image.image
imgCon = ccore.Image(imgRaw.width, imgRaw.height)
ccore.drawContour(oContainer.getBinary(), imgCon, 255,
False)
lstImages.append((imgRaw, strHexColor, 1.0))
lstImages.append((imgCon, strHexColor, fAlpha))
else:
for channel_name, dctChannelInfo in dctRenderInfo.iteritems():
if channel_name in self._channel_registry:
oChannel = self._channel_registry[channel_name]
if 'raw' in dctChannelInfo:
strHexColor, fAlpha = dctChannelInfo['raw']
# special casing for virtual channel to mix
# raw images together
if oChannel.is_virtual():
lstImages.extend(oChannel.meta_images(fAlpha))
else:
lstImages.append(
(oChannel.meta_image.image, strHexColor, 1.0))
if 'contours' in dctChannelInfo:
# transform the old dict-style to the new tuple-style,
# which allows multiple definitions for one region
if isinstance(dctChannelInfo['contours'], dict):
lstContourInfos = [
(k, ) + v for k, v in
dctChannelInfo['contours'].iteritems()
]
else:
lstContourInfos = dctChannelInfo['contours']
for tplData in lstContourInfos:
strRegion, strNameOrColor, fAlpha, bShowLabels = tplData[:
4]
# draw contours only if region is present
if oChannel.has_region(strRegion):
if len(tplData) > 4:
bThickContours = tplData[4]
else:
bThickContours = False
imgRaw = oChannel.meta_image.image
if strNameOrColor == 'class_label':
oContainer = oChannel.containers[strRegion]
oRegion = oChannel.get_region(strRegion)
dctLabels = {}
dctColors = {}
for iObjId, oObj in oRegion.iteritems():
iLabel = oObj.iLabel
if not iLabel is None:
if not iLabel in dctLabels:
dctLabels[iLabel] = []
dctLabels[iLabel].append(iObjId)
dctColors[
iLabel] = oObj.strHexColor
imgCon2 = ccore.Image(
imgRaw.width, imgRaw.height)
for iLabel, lstObjIds in dctLabels.iteritems(
):
imgCon = ccore.Image(
imgRaw.width, imgRaw.height)
# Flip this and use drawContours with fill option enables to get black background
oContainer.drawContoursByIds(
lstObjIds, 255, imgCon,
bThickContours, False)
# oContainer.drawContoursByIds(lstObjIds, 255, imgCon, bThickContours, True)
lstImages.append(
(imgCon, dctColors[iLabel],
fAlpha))
if isinstance(bShowLabels,
bool) and bShowLabels:
oContainer.drawTextsByIds(
lstObjIds,
[str(iLabel)] * len(lstObjIds),
imgCon2)
lstImages.append((imgCon2, '#FFFFFF', 1.0))
else:
oContainer = oChannel.containers[strRegion]
oRegion = oChannel.get_region(strRegion)
lstObjIds = oRegion.keys()
imgCon = ccore.Image(
imgRaw.width, imgRaw.height)
if not strNameOrColor is None:
oContainer.drawContoursByIds(
lstObjIds, 255, imgCon,
bThickContours, False)
else:
strNameOrColor = '#FFFFFF'
lstImages.append(
(imgCon, strNameOrColor, fAlpha))
if bShowLabels:
imgCon2 = ccore.Image(
imgRaw.width, imgRaw.height)
oContainer.drawLabelsByIds(
lstObjIds, imgCon2)
lstImages.append(
(imgCon2, '#FFFFFF', 1.0))
if len(lstImages) > 0:
imgRgb = ccore.makeRGBImage(
[x[0].getView() for x in lstImages],
[ccore.RGBValue(*hex2rgb(x[1]))
for x in lstImages], [x[2] for x in lstImages])
if writeToDisc:
strFilePath = join(
strPathOut,
"P%s_T%05d%s" % (self.P, self._iT, strFileSuffix))
makedirs(strPathOut)
ccore.writeImage(imgRgb, strFilePath, strCompression)
self.logger.debug("* rendered image written '%s'" %
strFilePath)
else:
strFilePath = ''
return imgRgb, strFilePath
def __init__(self, eventselector, strPathIn, oP, strPathOut,
imageCompression="85",
imageSuffix=".jpg",
border=0,
writeSubdirs=True,
writeDescription=True,
size=None,
oneFilePerTrack=False):
self._bHasImages = False
dctTimePoints = {}
for strStartId, lstTimeData in eventselector.bboxes( \
size=size, border=border).iteritems():
items = Tracker.split_nodeid(strStartId)
iStartT, iObjId = items[:2]
if len(items) == 3:
branch_id = items[2]
else:
branch_id = 1
if writeSubdirs:
strPathOutEvent = os.path.join(strPathOut,
self._format_name(oP, iStartT, iObjId, branch_id))
else:
strPathOutEvent = strPathOut
makedirs(strPathOutEvent)
if writeDescription:
oFile = file(os.path.join(strPathOutEvent,
"_%s.txt" % self._format_name(oP, iStartT, iObjId, branch_id)), "w")
lstData = ["Frame", "ObjId", "x1", "y1", "x2", "y2"]
oFile.write("%s\n" % "\t".join(map(str, lstData)))
for iCnt, (iT, tplBoundingBox, lstObjIds) in enumerate(lstTimeData):
if writeDescription:
lstData = [iT, ';'.join(map(str, lstObjIds))] + list(tplBoundingBox)
oFile.write("%s\n" % "\t".join(map(str, lstData)))
if not iT in dctTimePoints:
dctTimePoints[iT] = []
dctTimePoints[iT].append((strStartId, lstObjIds, iCnt, strPathOutEvent, tplBoundingBox))
if writeDescription:
oFile.close()
for idx, (iT, lstItems) in enumerate(dctTimePoints.iteritems()):
#print iT, lstItems
imgXY = self._getImage(strPathIn, iT)
for strStartId, lstObjIds, iCnt, strPathOutEvent, tplBoundingBox in lstItems:
x1, y1, x2, y2 = tplBoundingBox
x1Corr = 0 if x1 < 0 else x1
y1Corr = 0 if y1 < 0 else y1
x2Corr = imgXY.width-1 if x2 >= imgXY.width else x2
y2Corr = imgXY.height-1 if y2 >= imgXY.height else y2
imgSub = ccore.subImage(imgXY,
ccore.Diff2D(x1Corr, y1Corr),
ccore.Diff2D(x2Corr-x1Corr+1, y2Corr-y1Corr+1))
if (x1 < 0 or y1 < 0 or
x2 >= imgXY.width or y2 >= imgXY.height):
imgSub2 = self.IMAGE_CLASS(size[0], size[1])
ccore.copySubImage(imgSub, imgSub2, ccore.Diff2D(x1Corr-x1, y1Corr-y1))
imgSub = imgSub2
assert imgSub.width == size[0]
assert imgSub.width == x2-x1+1
assert imgSub.height == size[1]
assert imgSub.height == y2-y1+1
if self.PROCESS_LABEL:
lstImages = []
for iObjId in lstObjIds:
lstImages.append(ccore.copyImageIfLabel(imgSub, imgSub, iObjId))
imgSub = ccore.projectImage(lstImages, ccore.ProjectionType.MaxProjection)
strFilenameImage = os.path.join(strPathOutEvent, "P%s__T%05d%s" % (oP, iT, imageSuffix))
ccore.writeImage(imgSub, strFilenameImage)
if oneFilePerTrack and os.path.isdir(strPathOut):
self.convertToOneFilePerTrack(strPathOut, imageCompression)
def compose_galleries(path, path_hmm, quality="90",
one_daughter=True, sample=30):
logger = logging.getLogger('compose_galleries')
column_name = 'Trajectory'
path_index = os.path.join(path_hmm, '_index')
if not os.path.isdir(path_index):
logger.warning(("Index path '%s' does not exist. Make sure the error"
" correction was executed successfully." %path_index))
return
for filename in os.listdir(path_index):
logger.info('Creating gallery overview for %s' % filename)
group_name = os.path.splitext(filename)[0]
t = read_table(os.path.join(path_index, filename))[1]
t.reverse()
if one_daughter:
for record in t[:]:
if record[column_name].split('__')[4] != 'B01':
t.remove(record)
n = len(t)
if not sample is None and sample <= n:
idx = random.sample(xrange(n), sample)
idx.sort()
d = [t[i] for i in idx]
else:
d = t
n = len(d)
results = {}
for idx, record in enumerate(d):
#print idx, record
traj = record[column_name]
items = traj.split('__')
pos = items[1][1:]
key = '__'.join(items[1:5])
gallery_path = os.path.join(path, 'analyzed', pos, 'gallery')
if os.path.isdir(gallery_path):
for gallery_name in os.listdir(gallery_path):
img = ccore.readImageRGB(os.path.join(gallery_path, gallery_name, '%s.jpg' % key))
if gallery_name not in results:
results[gallery_name] = ccore.RGBImage(img.width, img.height*n)
img_out = results[gallery_name]
ccore.copySubImage(img,
ccore.Diff2D(0, 0),
ccore.Diff2D(img.width, img.height),
img_out,
ccore.Diff2D(0, img.height*idx))
for gallery_name in results:
path_out = os.path.join(path_hmm, '_gallery', gallery_name)
makedirs(path_out)
image_name = os.path.join(path_out, '%s.jpg' % group_name)
ccore.writeImage(results[gallery_name], image_name, quality)
logger.debug("Gallery image '%s' successfully written." % image_name)
yield group_name
def render(self, strPathOut, dctRenderInfo=None,
strFileSuffix='.jpg', strCompression='98', writeToDisc=True,
images=None):
lstImages = []
if not images is None:
lstImages += images
if dctRenderInfo is None:
for name, oChannel in self._channel_registry.iteritems():
for strRegion, oContainer in oChannel.containers.iteritems():
strHexColor, fAlpha = oChannel.dctAreaRendering[strRegion]
imgRaw = oChannel.meta_image.image
imgCon = ccore.Image(imgRaw.width, imgRaw.height)
ccore.drawContour(oContainer.getBinary(), imgCon, 255, False)
lstImages.append((imgRaw, strHexColor, 1.0))
lstImages.append((imgCon, strHexColor, fAlpha))
else:
for channel_name, dctChannelInfo in dctRenderInfo.iteritems():
if channel_name in self._channel_registry:
oChannel = self._channel_registry[channel_name]
if 'raw' in dctChannelInfo:
strHexColor, fAlpha = dctChannelInfo['raw']
# special casing for virtual channel to mix
# raw images together
if oChannel.is_virtual():
lstImages.extend(oChannel.meta_images(fAlpha))
else:
lstImages.append((oChannel.meta_image.image, strHexColor, 1.0))
if 'contours' in dctChannelInfo:
# transform the old dict-style to the new tuple-style,
# which allows multiple definitions for one region
if isinstance(dctChannelInfo['contours'], dict):
lstContourInfos = [(k,)+v
for k,v in dctChannelInfo['contours'].iteritems()]
else:
lstContourInfos = dctChannelInfo['contours']
for tplData in lstContourInfos:
strRegion, strNameOrColor, fAlpha, bShowLabels = tplData[:4]
# draw contours only if region is present
if oChannel.has_region(strRegion):
if len(tplData) > 4:
bThickContours = tplData[4]
else:
bThickContours = False
imgRaw = oChannel.meta_image.image
if strNameOrColor == 'class_label':
oContainer = oChannel.containers[strRegion]
oRegion = oChannel.get_region(strRegion)
dctLabels = {}
dctColors = {}
for iObjId, oObj in oRegion.iteritems():
iLabel = oObj.iLabel
if not iLabel is None:
if not iLabel in dctLabels:
dctLabels[iLabel] = []
dctLabels[iLabel].append(iObjId)
dctColors[iLabel] = oObj.strHexColor
imgCon2 = ccore.Image(imgRaw.width, imgRaw.height)
for iLabel, lstObjIds in dctLabels.iteritems():
imgCon = ccore.Image(imgRaw.width, imgRaw.height)
# Flip this and use drawContours with fill option enables to get black background
oContainer.drawContoursByIds(lstObjIds, 255, imgCon, bThickContours, False)
# oContainer.drawContoursByIds(lstObjIds, 255, imgCon, bThickContours, True)
lstImages.append((imgCon, dctColors[iLabel], fAlpha))
if isinstance(bShowLabels, bool) and bShowLabels:
oContainer.drawTextsByIds(lstObjIds, [str(iLabel)]*len(lstObjIds), imgCon2)
lstImages.append((imgCon2, '#FFFFFF', 1.0))
else:
oContainer = oChannel.containers[strRegion]
oRegion = oChannel.get_region(strRegion)
lstObjIds = oRegion.keys()
imgCon = ccore.Image(imgRaw.width, imgRaw.height)
if not strNameOrColor is None:
oContainer.drawContoursByIds(lstObjIds, 255, imgCon, bThickContours, False)
else:
strNameOrColor = '#FFFFFF'
lstImages.append((imgCon, strNameOrColor, fAlpha))
if bShowLabels:
imgCon2 = ccore.Image(imgRaw.width, imgRaw.height)
oContainer.drawLabelsByIds(lstObjIds, imgCon2)
lstImages.append((imgCon2, '#FFFFFF', 1.0))
if len(lstImages) > 0:
imgRgb = ccore.makeRGBImage([x[0].getView() for x in lstImages],
[ccore.RGBValue(*hex2rgb(x[1])) for x in lstImages],
[x[2] for x in lstImages])
if writeToDisc:
strFilePath = join(strPathOut, "P%s_T%05d%s"
%(self.P, self._iT, strFileSuffix))
makedirs(strPathOut)
ccore.writeImage(imgRgb, strFilePath, strCompression)
self.logger.debug("* rendered image written '%s'" % strFilePath)
else:
strFilePath = ''
return imgRgb, strFilePath
def cutTracks(self,
full_track_data,
img_container,
plate, pos,
lstTracks=None,
channels=None,
skip_done=False):
#imoutDir = self.oSettings.galleryDir
#inDir = os.path.join(self.oSettings.rawImgDir, plate)
#lstTracks.sort()
#imgContainer = self.imageImporter(inDir)
#channels = self.oSettings.plateChannelDict[plate].values()
#filter(lambda x: x.split('__')[0] != 'feature', impdata['plate1_1_013']['00008']['T00181__O0031']['primary']['primary'].keys())
#filter(lambda x: x.split('__')[0] != 'feature', impdata['plate1_1_013']['00008']['T00181__O0031']['primary']['primary'].keys())
#['tracking__upperleft_x', 'tracking__center_x', 'tracking__lowerright_y', 'class__label', 'class__name', 'tracking__lowerright_x', 'tracking__center_y', 'class__probability', 'tracking__upperleft_y']
if channels is None:
channels = img_container.meta_data.channels
imoutDir = os.path.join(self.baseOutDir, plate, pos)
if not os.path.exists(imoutDir):
print 'generating the folder %s' % imoutDir
os.makedirs(imoutDir)
if lstTracks is None:
lstTracks = sorted(full_track_data[plate][pos].keys())
for trackId in lstTracks:
center_values = zip(full_track_data[plate][pos][trackId][self.track_channel][self.track_region]['tracking__center_x'],
full_track_data[plate][pos][trackId][self.track_channel][self.track_region]['tracking__center_y'],
full_track_data[plate][pos][trackId][self.track_channel][self.track_region]['Frame'])
print 'cutting ', trackId
imout_filename = os.path.join(imoutDir, 'Gallery--%s.png' % (trackId))
if skip_done and os.path.isfile(imout_filename):
continue
# allocate output image
imout = ccore.Image(len(center_values) * (2*self.width + 1), len(channels) * (2*self.width + 1))
images = {}
x = 0
for cx, cy, timepoint in center_values:
y = 0
for channel in channels :
#image_filename = os.path.join(inDir, imageInfo[pos][timepoint][channel]['path'],
# imageInfo[pos][timepoint][channel]['filename'])
image_filename = os.path.join(img_container.path,
img_container.dimension_lookup[pos][timepoint][channel][0])
#print image_filename
imin = ccore.readImageMito(image_filename)
x_ul = cx - self.width if cx >= self.width else 0 # max(cx - width, 0)
#x_ul = max(cx - width, 0)
y_ul = cy - self.width if cy >= self.width else 0 # max(cy - width, 0)
#y_ul = max(cy - width, 0)
x_lr = cx + self.width if cx + self.width < imin.width else imin.width - 1
#x_lr = min(cx + width, imin.width-1)
y_lr = cy + self.width if cy + self.width < imin.height else imin.height - 1
#y_lr = min(cx + width, imin.height-1)
w_x = x_lr - x_ul
w_y = y_lr - y_ul
#print x_ul, y_ul, x_lr, y_lr, w_x, w_y
imsub = ccore.subImage(imin,
ccore.Diff2D(int(x_ul), int(y_ul)),
ccore.Diff2D(int(w_x), int(w_y)))
ccore.copySubImage(imsub, imout, ccore.Diff2D(x, y))
y += (2 * self.width + 1)
x += (2 * self.width + 1)
ccore.writeImage(imout, imout_filename)
return