def show_channels(path: Path = Depends(imagepath_parameter)):
"""
Get image channel info
"""
original = path.get_original()
check_representation_existence(original)
return response_list(ChannelsInfo.from_image(original))
def show_associated(path: Path = Depends(imagepath_parameter)):
"""
Get associated file info
"""
original = path.get_original()
check_representation_existence(original)
return response_list(AssociatedInfo.from_image(original))
def show_channels_histogram_bounds(
path: Path = Depends(imagepath_parameter),
channels: Optional[List[conint(ge=0)]] = Query(
None, description="Only return histograms for these channels"
),
):
"""
Get histogram bounds per channel where all planes (Z,T) are merged.
"""
in_image = path.get_spatial()
check_representation_existence(in_image)
channels = ensure_list(channels)
channels = get_channel_indexes(in_image, channels)
hist_info = []
htype = in_image.histogram_type()
hist_filter = operator.itemgetter(*channels)
channels_bounds = hist_filter(in_image.channels_bounds())
if len(channels) == 1:
channels_bounds = [channels_bounds]
for channel, bounds in zip(channels, channels_bounds):
mini, maxi = bounds
hist_info.append(
ChannelHistogramInfo(
channel=channel, type=htype,
color=in_image.channels[channel].hex_color,
minimum=mini, maximum=maxi
)
)
return response_list(hist_info)
def show_plane_histogram(
z_slices: conint(ge=0),
timepoints: conint(ge=0),
path: Path = Depends(imagepath_parameter),
channels: Optional[List[conint(ge=0)]] = Query(
None, description="Only return histograms for these channels"
),
):
"""
Get histogram per plane.
"""
in_image = path.get_spatial()
check_representation_existence(in_image)
channels = ensure_list(channels)
z_slices = ensure_list(z_slices)
timepoints = ensure_list(timepoints)
channels = get_channel_indexes(in_image, channels)
z_slices = get_zslice_indexes(in_image, z_slices)
timepoints = get_timepoint_indexes(in_image, timepoints)
hist_info = []
htype = in_image.histogram_type()
for c, z, t in itertools.product(channels, z_slices, timepoints):
mini, maxi = in_image.plane_bounds(c, z, t)
hist_info.append(
PlaneHistogramInfo(
channel=c, z_slice=z, timepoint=t, type=htype,
color=in_image.channels[c].hex_color,
minimum=mini, maximum=maxi
)
)
return response_list(hist_info)
def list_representations(path: Path = Depends(imagepath_parameter)):
"""
Get all image representation info
"""
return response_list([
RepresentationInfo.from_path(rpr)
for rpr in path.get_representations()
])
def show_metadata(path: Path = Depends(imagepath_parameter)):
"""
Get image metadata
"""
original = path.get_original()
check_representation_existence(original)
store = original.raw_metadata
return response_list([Metadata.from_metadata(md) for md in store.values()])
def show_metadata_annotations(path: Path = Depends(imagepath_parameter)):
"""
Get image annotation metadata
"""
original = path.get_original()
check_representation_existence(original)
return response_list([
MetadataAnnotation.from_metadata_annotation(a)
for a in original.annotations
])
def list_colormaps(with_inverted: bool = Query(
False, description="Also list inverted colormaps")):
"""
List all colormaps
"""
colormaps = [
_serialize_colormap(cmap) for cmap in COLORMAPS.values()
if with_inverted or not cmap.inverted
]
return response_list(colormaps)
def show_plane_histogram(
z_slices: conint(ge=0),
timepoints: conint(ge=0),
path: Path = Depends(imagepath_parameter),
hist_config: HistogramConfig = Depends(),
channels: Optional[List[conint(ge=0)]] = Query(
None, description="Only return histograms for these channels"
),
):
"""
Get histogram per plane.
"""
in_image = path.get_spatial()
check_representation_existence(in_image)
channels = ensure_list(channels)
z_slices = ensure_list(z_slices)
timepoints = ensure_list(timepoints)
channels = get_channel_indexes(in_image, channels)
z_slices = get_zslice_indexes(in_image, z_slices)
timepoints = get_timepoint_indexes(in_image, timepoints)
histograms = []
n_bins = parse_n_bins(hist_config.n_bins, len(in_image.value_range))
htype = in_image.histogram_type()
for c, z, t in itertools.product(channels, z_slices, timepoints):
histograms.append(
PlaneHistogram(
channel=c, z_slice=z, timepoint=t, type=htype,
color=in_image.channels[c].hex_color,
**histogram_formatter(
in_image.plane_histogram(c, z, t),
in_image.plane_bounds(c, z, t),
n_bins, hist_config.full_range
)
)
)
return response_list(histograms)
def show_channels_histogram(
path: Path = Depends(imagepath_parameter),
hist_config: HistogramConfig = Depends(),
channels: Optional[List[conint(ge=0)]] = Query(
None, description="Only return histograms for these channels"
),
):
"""
Get histograms per channel where all planes (Z,T) are merged.
"""
in_image = path.get_spatial()
check_representation_existence(in_image)
channels = ensure_list(channels)
channels = get_channel_indexes(in_image, channels)
histograms = []
n_bins = parse_n_bins(hist_config.n_bins, len(in_image.value_range))
htype = in_image.histogram_type()
# hist_filter = operator.itemgetter(*channels)
# channels_bounds = hist_filter(in_image.channels_bounds())
# channels_histograms = hist_filter(in_image.channel_histogram()) TODO
for channel in channels:
histograms.append(
ChannelHistogram(
channel=channel, type=htype,
color=in_image.channels[channel].hex_color,
**histogram_formatter(
in_image.channel_histogram(channel),
in_image.channel_bounds(channel),
n_bins, hist_config.full_range
)
)
)
return response_list(histograms)
def list_filters():
"""
List all filters
"""
filters = [_serialize_filter(imgfilter) for imgfilter in FILTERS.values()]
return response_list(filters)
def list_formats():
"""
List all formats
"""
formats = [_serialize_format(format) for format in FORMATS.values()]
return response_list(formats)