def apply_registration(self):
img_in = self.meta_image.image
image = ccore.subImage(img_in,
ccore.Diff2D(*self.registration_start)-
ccore.Diff2D(*self.channelRegistration),
ccore.Diff2D(*self.new_image_size))
self.meta_image.set_image(image)
def normalize_image(self, plate_id=None):
img_in = self.meta_image.image
if self.bFlatfieldCorrection:
self.logger.debug("* using flat field correction with image from %s"
% self.strBackgroundImagePath)
imgBackground = self._load_flatfield_correction_image(plate_id)
crop_coordinated = MetaImage.get_crop_coordinates()
if crop_coordinated is not None:
self.logger.debug("* applying cropping to background image")
imgBackground = ccore.subImage(imgBackground,
ccore.Diff2D(crop_coordinated[0],
crop_coordinated[1]),
ccore.Diff2D(crop_coordinated[2],
crop_coordinated[3]))
img_in = ccore.flatfieldCorrection(img_in, imgBackground, 0.0, True)
img_out = ccore.linearTransform2(img_in, self.fNormalizeMin,
self.fNormalizeMax, 0, 255, 0, 255)
else:
self.logger.debug("* not using flat field correction")
if type(img_in) == ccore.UInt16Image:
img_out = ccore.linearTransform3(img_in, int(self.fNormalizeMin),
int(self.fNormalizeMax),
0, 255, 0, 255)
elif type(img_in) == ccore.Image:
img_out = ccore.linearTransform2(img_in, int(self.fNormalizeMin),
int(self.fNormalizeMax),
0, 255, 0, 255)
else:
img_out = img_in
self.meta_image.set_image(img_out)
def _cropped_image(self):
if self._img_c is None:
self._img_c = ccore.subImage(
self._raw_image, ccore.Diff2D(MetaImage._crop_coordinates[0],
MetaImage._crop_coordinates[1]),
ccore.Diff2D(MetaImage._crop_coordinates[2],
MetaImage._crop_coordinates[3]))
return self._img_c
def _cropped_image(self):
if self._img_c is None:
self._img_c = ccore.subImage(
self._raw_image, ccore.Diff2D(MetaImage._crop_coordinates[0],
MetaImage._crop_coordinates[1]),
ccore.Diff2D(MetaImage._crop_coordinates[2],
MetaImage._crop_coordinates[3]))
return self._img_c
def _on_update_image(self, image_rgb, info, filename):
if self._show_image.isChecked():
# FIXME:
if image_rgb.width % 4 != 0:
image_rgb = ccore.subImage(
image_rgb, ccore.Diff2D(0,0), ccore.Diff2D(image_rgb.width - \
(image_rgb.width % 4), image_rgb.height))
qimage = numpy_to_qimage(image_rgb.toArray(copy=False))
if qApp._image_dialog is None:
qApp._image_dialog = QFrame()
ratio = qimage.height() / float(qimage.width())
qApp._image_dialog.setGeometry(50, 50, 800, 800 * ratio)
shortcut = QShortcut(QKeySequence(Qt.Key_Escape),
qApp._image_dialog)
shortcut.activated.connect(self._on_esc_pressed)
layout = QVBoxLayout(qApp._image_dialog)
layout.setContentsMargins(0, 0, 0, 0)
qApp._graphics = ImageRatioDisplay(qApp._image_dialog, ratio)
qApp._graphics.setScaledContents(True)
qApp._graphics.resize(800, 800 * ratio)
qApp._graphics.setMinimumSize(QSize(100, 100))
policy = QSizePolicy(QSizePolicy.Expanding,
QSizePolicy.Expanding)
policy.setHeightForWidth(True)
qApp._graphics.setSizePolicy(policy)
layout.addWidget(qApp._graphics)
dummy = QFrame(qApp._image_dialog)
dymmy_layout = QHBoxLayout(dummy)
dymmy_layout.setContentsMargins(5, 5, 5, 5)
qApp._image_combo = QComboBox(dummy)
qApp._image_combo.setSizePolicy(
QSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed))
self._set_display_renderer_info()
dymmy_layout.addStretch()
dymmy_layout.addWidget(qApp._image_combo)
dymmy_layout.addStretch()
layout.addWidget(dummy)
layout.addStretch()
qApp._image_dialog.show()
qApp._image_dialog.raise_()
#else:
# qApp._graphics_pixmap.setPixmap(QPixmap.fromImage(qimage))
qApp._graphics.setPixmap(QPixmap.fromImage(qimage))
qApp._image_dialog.setWindowTitle(info)
qApp._image_dialog.setToolTip(filename)
if not qApp._image_dialog.isVisible():
qApp._image_dialog.show()
qApp._image_dialog.raise_()
def apply_registration(self):
img_in = self.meta_image.image
# ccore.subImage checks dimensions
image = ccore.subImage(
img_in,
ccore.Diff2D(*self.registration_start) -
ccore.Diff2D(*self.channelRegistration),
ccore.Diff2D(*self.new_image_size))
self.meta_image.set_image(image)
def _on_update_image(self, image_rgb, info, filename):
if self._show_image.isChecked():
# FIXME:
if image_rgb.width % 4 != 0:
image_rgb = ccore.subImage(
image_rgb, ccore.Diff2D(0,0), ccore.Diff2D(image_rgb.width - \
(image_rgb.width % 4), image_rgb.height))
qimage = numpy_to_qimage(image_rgb.toArray(copy=False))
if qApp._image_dialog is None:
qApp._image_dialog = QFrame()
ratio = qimage.height()/float(qimage.width())
qApp._image_dialog.setGeometry(50, 50, 800, 800*ratio)
shortcut = QShortcut(QKeySequence(Qt.Key_Escape), qApp._image_dialog)
shortcut.activated.connect(self._on_esc_pressed)
layout = QVBoxLayout(qApp._image_dialog)
layout.setContentsMargins(0,0,0,0)
qApp._graphics = ImageRatioDisplay(qApp._image_dialog, ratio)
qApp._graphics.setScaledContents(True)
qApp._graphics.resize(800, 800*ratio)
qApp._graphics.setMinimumSize(QSize(100,100))
policy = QSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
policy.setHeightForWidth(True)
qApp._graphics.setSizePolicy(policy)
layout.addWidget(qApp._graphics)
dummy = QFrame(qApp._image_dialog)
dymmy_layout = QHBoxLayout(dummy)
dymmy_layout.setContentsMargins(5,5,5,5)
qApp._image_combo = QComboBox(dummy)
qApp._image_combo.setSizePolicy(QSizePolicy(QSizePolicy.Expanding,
QSizePolicy.Fixed))
self._set_display_renderer_info()
dymmy_layout.addStretch()
dymmy_layout.addWidget(qApp._image_combo)
dymmy_layout.addStretch()
layout.addWidget(dummy)
layout.addStretch()
qApp._image_dialog.show()
qApp._image_dialog.raise_()
#else:
# qApp._graphics_pixmap.setPixmap(QPixmap.fromImage(qimage))
qApp._graphics.setPixmap(QPixmap.fromImage(qimage))
qApp._image_dialog.setWindowTitle(info)
qApp._image_dialog.setToolTip(filename)
if not qApp._image_dialog.isVisible():
qApp._image_dialog.show()
qApp._image_dialog.raise_()
def normalize_image(self, plate_id=None):
try:
import pydevd
pydevd.connected = True
pydevd.settrace(suspend=False)
print 'Thread enabled interactive eclipse debuging...'
except:
pass
img_in = self.meta_image.image
if self.bFlatfieldCorrection:
self.logger.debug(
"* using flat field correction with image from %s" %
self.strBackgroundImagePath)
imgBackground = self._load_flatfield_correction_image(plate_id)
crop_coordinated = MetaImage.get_crop_coordinates()
if crop_coordinated is not None:
self.logger.debug("* applying cropping to background image")
imgBackground = ccore.subImage(
imgBackground,
ccore.Diff2D(crop_coordinated[0], crop_coordinated[1]),
ccore.Diff2D(crop_coordinated[2], crop_coordinated[3]))
img_in = ccore.flatfieldCorrection(img_in, imgBackground, 0.0,
True)
img_out = ccore.linearTransform2(img_in, self.fNormalizeMin,
self.fNormalizeMax, 0, 255, 0,
255)
else:
self.logger.debug("* not using flat field correction")
if type(img_in) == ccore.UInt16Image:
img_out = ccore.linearTransform3(img_in,
int(self.fNormalizeMin),
int(self.fNormalizeMax), 0,
255, 0, 255)
elif type(img_in) == ccore.Image:
img_out = ccore.linearTransform2(img_in,
int(self.fNormalizeMin),
int(self.fNormalizeMax), 0,
255, 0, 255)
else:
img_out = img_in
self.meta_image.set_image(img_out)
def normalize_image(self, plate_id=None):
try:
import pydevd
pydevd.connected = True
pydevd.settrace(suspend=False)
print 'Thread enabled interactive eclipse debuging...'
except:
pass
img_in = self.meta_image.image
if self.bFlatfieldCorrection:
self.logger.debug("* using flat field correction with image from %s"
% self.strBackgroundImagePath)
imgBackground = self._load_flatfield_correction_image(plate_id)
crop_coordinated = MetaImage.get_crop_coordinates()
if crop_coordinated is not None:
self.logger.debug("* applying cropping to background image")
imgBackground = ccore.subImage(imgBackground,
ccore.Diff2D(crop_coordinated[0],
crop_coordinated[1]),
ccore.Diff2D(crop_coordinated[2],
crop_coordinated[3]))
img_in = ccore.flatfieldCorrection(img_in, imgBackground, 0.0, True)
img_out = ccore.linearTransform2(img_in, self.fNormalizeMin,
self.fNormalizeMax, 0, 255, 0, 255)
else:
self.logger.debug("* not using flat field correction")
if type(img_in) == ccore.UInt16Image:
img_out = ccore.linearTransform3(img_in, int(self.fNormalizeMin),
int(self.fNormalizeMax),
0, 255, 0, 255)
elif type(img_in) == ccore.Image:
img_out = ccore.linearTransform2(img_in, int(self.fNormalizeMin),
int(self.fNormalizeMax),
0, 255, 0, 255)
else:
img_out = img_in
self.meta_image.set_image(img_out)
def normalize_image(self, plate_id=None):
img_in = self.meta_image.image
if self.bFlatfieldCorrection:
self.logger.debug(
"* using flat field correction with image from %s" %
self.strBackgroundImagePath)
imgBackground = self._load_flatfield_correction_image(plate_id)
crop_coordinated = MetaImage.get_crop_coordinates()
if crop_coordinated is not None:
self.logger.debug("* applying cropping to background image")
imgBackground = ccore.subImage(
imgBackground,
ccore.Diff2D(crop_coordinated[0], crop_coordinated[1]),
ccore.Diff2D(crop_coordinated[2], crop_coordinated[3]))
img_in = ccore.flatfieldCorrection(img_in, imgBackground, 0.0,
True)
img_out = ccore.linearTransform2(img_in, self.fNormalizeMin,
self.fNormalizeMax, 0, 255, 0,
255)
else:
self.logger.debug("* not using flat field correction")
if type(img_in) == ccore.UInt16Image:
img_out = ccore.linearTransform3(img_in,
int(self.fNormalizeMin),
int(self.fNormalizeMax), 0,
255, 0, 255)
elif type(img_in) == ccore.Image:
img_out = ccore.linearTransform2(img_in,
int(self.fNormalizeMin),
int(self.fNormalizeMax), 0,
255, 0, 255)
else:
img_out = img_in
self.meta_image.set_image(img_out)
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 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
