def imgData_json(request, imageId, conn=None, **kwargs):
image = conn.getObject("Image", imageId)
if image is None:
raise Http404("Image not found")
rv = imageMarshal(image)
sizeT = image.getSizeT()
timeList = []
if sizeT > 1:
params = omero.sys.ParametersI()
params.addLong('pid', image.getPixelsId())
query = "from PlaneInfo as Info where"\
" Info.theZ=0 and Info.theC=0 and pixels.id=:pid"
infoList = conn.getQueryService().findAllByQuery(
query, params, conn.SERVICE_OPTS)
timeMap = {}
for info in infoList:
tIndex = info.theT.getValue()
time = int(info.deltaT.getValue())
timeMap[tIndex] = time
for t in range(image.getSizeT()):
if t in timeMap:
timeList.append(timeMap[t])
rv['deltaT'] = timeList
return HttpResponse(json.dumps(rv), content_type='json')
def img_data_json(request, image_id, conn=None, **kwargs):
image = conn.getObject("Image", image_id)
if image is None:
raise Http404("Image not found")
# Test if we have Units support (OMERO 5.1)
px = image.getPrimaryPixels().getPhysicalSizeX()
pix_size_x = str(px) # As string E.g. "0.13262 MICROMETER"
units_support = " " in pix_size_x
rv = imageMarshal(image)
if units_support:
# Add extra parameters with units data
# NB ['pixel_size']['x'] will have size in MICROMETER
px = image.getPrimaryPixels().getPhysicalSizeX()
rv['pixel_size']['valueX'] = px.getValue()
rv['pixel_size']['symbolX'] = px.getSymbol()
rv['pixel_size']['unitX'] = str(px.getUnit())
py = image.getPrimaryPixels().getPhysicalSizeY()
rv['pixel_size']['valueY'] = py.getValue()
rv['pixel_size']['symbolY'] = py.getSymbol()
rv['pixel_size']['unitY'] = str(py.getUnit())
size_t = image.getSizeT()
time_list = []
if size_t > 1:
time_list = get_timestamps(conn, image)
rv['deltaT'] = time_list
return HttpResponse(json.dumps(rv), content_type='json')
def image_data(request, image_id, conn=None, **kwargs):
image = conn.getObject("Image", image_id)
if image is None:
return JsonResponse({"error": "Image not found"}, status=404)
try:
rv = imageMarshal(image)
# set roi count
rv['roi_count'] = image.getROICount()
# Add extra parameters with units data
# Note ['pixel_size']['x'] will have size in MICROMETER
px = image.getPrimaryPixels().getPhysicalSizeX()
if (px is not None):
size = image.getPixelSizeX(True)
value = format_pixel_size_with_units(size)
rv['pixel_size']['unit_x'] = value[0]
rv['pixel_size']['symbol_x'] = value[1]
py = image.getPrimaryPixels().getPhysicalSizeY()
if (py is not None):
size = image.getPixelSizeY(True)
value = format_pixel_size_with_units(size)
rv['pixel_size']['unit_y'] = value[0]
rv['pixel_size']['symbol_y'] = value[1]
pz = image.getPrimaryPixels().getPhysicalSizeZ()
if (pz is not None):
size = image.getPixelSizeZ(True)
value = format_pixel_size_with_units(size)
rv['pixel_size']['unit_z'] = value[0]
rv['pixel_size']['symbol_z'] = value[1]
delta_t_unit_symbol = None
rv['delta_t_unit_symbol'] = delta_t_unit_symbol
df = "%Y-%m-%d %H:%M:%S"
rv['import_date'] = image.creationEventDate().strftime(df)
if image.getAcquisitionDate() is not None:
rv['acquisition_date'] = image.getAcquisitionDate().strftime(df)
# add available families
rv['families'] = []
families = image.getFamilies().values()
for fam in families:
rv['families'].append(fam.getValue())
return JsonResponse(rv)
except Exception as image_data_retrieval_exception:
return JsonResponse({'error': repr(image_data_retrieval_exception)})
def img_data_json(request, image_id, conn=None, **kwargs):
image = conn.getObject("Image", image_id)
if image is None:
raise Http404("Image not found")
# Test if we have Units support (OMERO 5.1)
px = image.getPrimaryPixels().getPhysicalSizeX()
pix_size_x = str(px) # As string E.g. "0.13262 MICROMETER"
units_support = " " in pix_size_x
rv = imageMarshal(image)
if units_support:
# Add extra parameters with units data
# NB ['pixel_size']['x'] will have size in MICROMETER
px = image.getPrimaryPixels().getPhysicalSizeX()
rv['pixel_size']['valueX'] = px.getValue()
rv['pixel_size']['symbolX'] = px.getSymbol()
rv['pixel_size']['unitX'] = str(px.getUnit())
py = image.getPrimaryPixels().getPhysicalSizeY()
rv['pixel_size']['valueY'] = py.getValue()
rv['pixel_size']['symbolY'] = py.getSymbol()
rv['pixel_size']['unitY'] = str(py.getUnit())
size_t = image.getSizeT()
time_list = []
if size_t > 1:
params = omero.sys.ParametersI()
params.addLong('pid', image.getPixelsId())
query = "from PlaneInfo as Info where"\
" Info.theZ=0 and Info.theC=0 and pixels.id=:pid"
info_list = conn.getQueryService().findAllByQuery(
query, params, conn.SERVICE_OPTS)
timemap = {}
for info in info_list:
t_index = info.theT.getValue()
if info.deltaT is not None:
# planeInfo.deltaT gives number only (no units)
# Therefore compatible with OMERO 5.0 and 5.1
delta_t = int(round(info.deltaT.getValue()))
timemap[t_index] = delta_t
for t in range(image.getSizeT()):
if t in timemap:
time_list.append(timemap[t])
rv['deltaT'] = time_list
return HttpResponse(json.dumps(rv), content_type='json')
def img_data_json(request, image_id, conn=None, **kwargs):
image = conn.getObject("Image", image_id)
if image is None:
raise Http404("Image not found")
# Test if we have Units support (OMERO 5.1)
px = image.getPrimaryPixels().getPhysicalSizeX()
pix_size_x = str(px) # As string E.g. "0.13262 MICROMETER"
units_support = " " in pix_size_x
rv = imageMarshal(image)
if units_support:
# Add extra parameters with units data
# NB ['pixel_size']['x'] will have size in MICROMETER
px = image.getPrimaryPixels().getPhysicalSizeX()
rv['pixel_size']['valueX'] = px.getValue()
rv['pixel_size']['symbolX'] = px.getSymbol()
rv['pixel_size']['unitX'] = str(px.getUnit())
py = image.getPrimaryPixels().getPhysicalSizeY()
rv['pixel_size']['valueY'] = py.getValue()
rv['pixel_size']['symbolY'] = py.getSymbol()
rv['pixel_size']['unitY'] = str(py.getUnit())
size_t = image.getSizeT()
time_list = []
if size_t > 1:
params = omero.sys.ParametersI()
params.addLong('pid', image.getPixelsId())
query = "from PlaneInfo as Info where"\
" Info.theZ=0 and Info.theC=0 and pixels.id=:pid"
info_list = conn.getQueryService().findAllByQuery(
query, params, conn.SERVICE_OPTS)
timemap = {}
for info in info_list:
t_index = info.theT.getValue()
if info.deltaT is not None:
# planeInfo.deltaT gives number only (no units)
# Therefore compatible with OMERO 5.0 and 5.1
delta_t = int(round(info.deltaT.getValue()))
timemap[t_index] = delta_t
for t in range(image.getSizeT()):
if t in timemap:
time_list.append(timemap[t])
rv['deltaT'] = time_list
return HttpResponse(json.dumps(rv), content_type='json')
def image_data(request, image_id, conn=None, **kwargs):
image = conn.getObject("Image", image_id)
if image is None:
return JsonResponse({"error": "Image not found"}, status=404)
try:
desc = image.getDescription()
if len(desc) <= 0:
image.setDescription('1')
image.save()
desc = '1'
rv = imageMarshal(image)
rv['isAdmin'] = conn.isAdmin()
rv['curUserId'] = conn.getUserId()
rv['curStep'] = int(desc)
# set roi count
rv['roi_count'] = image.getROICount()
# Add extra parameters with units data
# Note ['pixel_size']['x'] will have size in MICROMETER
px = image.getPrimaryPixels().getPhysicalSizeX()
if (px is not None):
size = image.getPixelSizeX(True)
value = format_value_with_units(size)
rv['pixel_size']['unit_x'] = value[0]
rv['pixel_size']['symbol_x'] = value[1]
py = image.getPrimaryPixels().getPhysicalSizeY()
if (py is not None):
size = image.getPixelSizeY(True)
value = format_value_with_units(size)
rv['pixel_size']['unit_y'] = value[0]
rv['pixel_size']['symbol_y'] = value[1]
pz = image.getPrimaryPixels().getPhysicalSizeZ()
if (pz is not None):
size = image.getPixelSizeZ(True)
value = format_value_with_units(size)
rv['pixel_size']['unit_z'] = value[0]
rv['pixel_size']['symbol_z'] = value[1]
size_t = image.getSizeT()
time_list = []
delta_t_unit_symbol = None
if size_t > 1:
params = omero.sys.ParametersI()
params.addLong('pid', image.getPixelsId())
z = 0
c = 0
query = "from PlaneInfo as Info where"\
" Info.theZ=%s and Info.theC=%s and pixels.id=:pid" % (z, c)
info_list = conn.getQueryService().findAllByQuery(
query, params, conn.SERVICE_OPTS)
timemap = {}
for info in info_list:
t_index = info.theT.getValue()
if info.deltaT is not None:
value = format_value_with_units(info.deltaT)
timemap[t_index] = value[0]
if delta_t_unit_symbol is None:
delta_t_unit_symbol = value[1]
for t in range(image.getSizeT()):
if t in timemap:
time_list.append(timemap[t])
rv['delta_t'] = time_list
rv['delta_t_unit_symbol'] = delta_t_unit_symbol
df = "%Y-%m-%d %H:%M:%S"
rv['import_date'] = image.creationEventDate().strftime(df)
if image.getAcquisitionDate() is not None:
rv['acquisition_date'] = image.getAcquisitionDate().strftime(df)
# add available families
rv['families'] = []
families = image.getFamilies().values()
for fam in families:
rv['families'].append(fam.getValue())
# rv['perms']['canAnnotate']= True
return JsonResponse(rv)
except Exception as image_data_retrieval_exception:
return JsonResponse({'error': repr(image_data_retrieval_exception)})
def image_data(request, image_id, conn=None, **kwargs):
image = conn.getObject("Image", image_id)
if image is None:
return JsonResponse({"error": "Image not found"}, status=404)
try:
rv = imageMarshal(image)
# Add extra parameters with units data
# Note ['pixel_size']['x'] will have size in MICROMETER
px = image.getPrimaryPixels().getPhysicalSizeX()
if (px is not None):
size = image.getPixelSizeX(True)
value = format_value_with_units(size)
rv['pixel_size']['unit_x'] = value[0]
rv['pixel_size']['symbol_x'] = value[1]
py = image.getPrimaryPixels().getPhysicalSizeY()
if (py is not None):
size = image.getPixelSizeY(True)
value = format_value_with_units(size)
rv['pixel_size']['unit_y'] = value[0]
rv['pixel_size']['symbol_y'] = value[1]
pz = image.getPrimaryPixels().getPhysicalSizeZ()
if (pz is not None):
size = image.getPixelSizeZ(True)
value = format_value_with_units(size)
rv['pixel_size']['unit_z'] = value[0]
rv['pixel_size']['symbol_z'] = value[1]
size_t = image.getSizeT()
time_list = []
delta_t_unit_symbol = None
if size_t > 1:
params = omero.sys.ParametersI()
params.addLong('pid', image.getPixelsId())
z = 0
c = 0
query = "from PlaneInfo as Info where"\
" Info.theZ=%s and Info.theC=%s and pixels.id=:pid" % (z, c)
info_list = conn.getQueryService().findAllByQuery(
query, params, conn.SERVICE_OPTS)
timemap = {}
for info in info_list:
t_index = info.theT.getValue()
if info.deltaT is not None:
value = format_value_with_units(info.deltaT)
timemap[t_index] = value[0]
if delta_t_unit_symbol is None:
delta_t_unit_symbol = value[1]
for t in range(image.getSizeT()):
if t in timemap:
time_list.append(timemap[t])
rv['delta_t'] = time_list
rv['delta_t_unit_symbol'] = delta_t_unit_symbol
return JsonResponse(rv)
except Exception as image_data_retrieval_exception:
return JsonResponse({'error': repr(image_data_retrieval_exception)})
