Extract metadata for scans generated by Prairie View acquisition software.
The Prairie View software generates one .ome.tif imaging file per frame
acquired. The metadata for all frames is contained in one .xml file. This
function locates the .xml file and generates a dictionary necessary to
populate the DataJoint ScanInfo and Field tables. Prairie View works
with resonance scanners with a single field. Prairie View does not support
bidirectional x and y scanning. ROI information is not contained in the
.xml file. All images generated using Prairie View have square dimensions(e.g. 512x512).
Parameters:
| Name |
Type |
Description |
Default |
ome_tif_filepath |
str
|
An absolute path to the .ome.tif image file.
|
required
|
Raises:
| Type |
Description |
FileNotFoundError
|
No .xml file containing information about the acquired scan
was found at path in parent directory at ome_tif_filepath.
|
Returns:
| Name | Type |
Description |
metainfo |
dict
|
A dict mapping keys to corresponding metadata values fetched from the
.xml file.
|
Source code in element_interface/prairie_view_loader.py
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200 | def get_prairieview_metadata(ome_tif_filepath: str) -> dict:
"""Extract metadata for scans generated by Prairie View acquisition software.
The Prairie View software generates one `.ome.tif` imaging file per frame
acquired. The metadata for all frames is contained in one .xml file. This
function locates the .xml file and generates a dictionary necessary to
populate the DataJoint `ScanInfo` and `Field` tables. Prairie View works
with resonance scanners with a single field. Prairie View does not support
bidirectional x and y scanning. ROI information is not contained in the
`.xml` file. All images generated using Prairie View have square dimensions(e.g. 512x512).
Args:
ome_tif_filepath: An absolute path to the .ome.tif image file.
Raises:
FileNotFoundError: No .xml file containing information about the acquired scan
was found at path in parent directory at `ome_tif_filepath`.
Returns:
metainfo: A dict mapping keys to corresponding metadata values fetched from the
.xml file.
"""
# May return multiple xml files. Only need one that contains scan metadata.
xml_files_list = pathlib.Path(ome_tif_filepath).parent.glob("*.xml")
for file in xml_files_list:
xml_tree = ET.parse(file)
xml_file = xml_tree.getroot()
if xml_file.find(".//Sequence"):
break
else:
raise FileNotFoundError(
f"No PrarieView metadata .xml file found at {pathlib.Path(ome_tif_filepath).parent}"
)
bidirectional_scan = False # Does not support bidirectional
roi = 0
n_fields = 1 # Always contains 1 field
recording_start_time = xml_file.find(".//Sequence/[@cycle='1']").attrib.get("time")
# Get all channels and find unique values
channel_list = [
int(channel.attrib.get("channel"))
for channel in xml_file.iterfind(".//Sequence/Frame/File/[@channel]")
]
n_channels = len(set(channel_list))
n_frames = len(xml_file.findall(".//Sequence/Frame"))
framerate = 1 / float(
xml_file.findall('.//PVStateValue/[@key="framePeriod"]')[0].attrib.get("value")
) # rate = 1/framePeriod
usec_per_line = (
float(
xml_file.findall(".//PVStateValue/[@key='scanLinePeriod']")[0].attrib.get(
"value"
)
)
* 1e6
) # Convert from seconds to microseconds
scan_datetime = datetime.strptime(
xml_file.attrib.get("date"), "%m/%d/%Y %I:%M:%S %p"
)
total_scan_duration = float(
xml_file.findall(".//Sequence/Frame")[-1].attrib.get("relativeTime")
)
pixel_height = int(
xml_file.findall(".//PVStateValue/[@key='pixelsPerLine']")[0].attrib.get(
"value"
)
)
# All PrairieView-acquired images have square dimensions (512 x 512; 1024 x 1024)
pixel_width = pixel_height
um_per_pixel = float(
xml_file.find(
".//PVStateValue/[@key='micronsPerPixel']/IndexedValue/[@index='XAxis']"
).attrib.get("value")
)
um_height = um_width = float(pixel_height) * um_per_pixel
# x and y coordinate values for the center of the field
x_field = float(
xml_file.find(
".//PVStateValue/[@key='currentScanCenter']/IndexedValue/[@index='XAxis']"
).attrib.get("value")
)
y_field = float(
xml_file.find(
".//PVStateValue/[@key='currentScanCenter']/IndexedValue/[@index='YAxis']"
).attrib.get("value")
)
if (
xml_file.find(
".//Sequence/[@cycle='1']/Frame/PVStateShard/PVStateValue/[@key='positionCurrent']/SubindexedValues/[@index='ZAxis']"
)
is None
):
z_fields = np.float64(
xml_file.find(
".//PVStateValue/[@key='positionCurrent']/SubindexedValues/[@index='ZAxis']/SubindexedValue"
).attrib.get("value")
)
n_depths = 1
assert z_fields.size == n_depths
bidirection_z = False
else:
bidirection_z = (
xml_file.find(".//Sequence").attrib.get("bidirectionalZ") == "True"
)
# One "Frame" per depth in the .xml file. Gets number of frames in first sequence
planes = [
int(plane.attrib.get("index"))
for plane in xml_file.findall(".//Sequence/[@cycle='1']/Frame")
]
n_depths = len(set(planes))
z_controllers = xml_file.findall(
".//Sequence/[@cycle='1']/Frame/[@index='1']/PVStateShard/PVStateValue/[@key='positionCurrent']/SubindexedValues/[@index='ZAxis']/SubindexedValue"
)
# If more than one Z-axis controllers are found,
# check which controller is changing z_field depth. Only 1 controller
# must change depths.
if len(z_controllers) > 1:
z_repeats = []
for controller in xml_file.findall(
".//Sequence/[@cycle='1']/Frame/[@index='1']/PVStateShard/PVStateValue/[@key='positionCurrent']/SubindexedValues/[@index='ZAxis']/"
):
z_repeats.append(
[
float(z.attrib.get("value"))
for z in xml_file.findall(
".//Sequence/[@cycle='1']/Frame/PVStateShard/PVStateValue/[@key='positionCurrent']/SubindexedValues/[@index='ZAxis']/SubindexedValue/[@subindex='{0}']".format(
controller.attrib.get("subindex")
)
)
]
)
controller_assert = [
not all(z == z_controller[0] for z in z_controller)
for z_controller in z_repeats
]
assert (
sum(controller_assert) == 1
), "Multiple controllers changing z depth is not supported"
z_fields = z_repeats[controller_assert.index(True)]
else:
z_fields = [
z.attrib.get("value")
for z in xml_file.findall(
".//Sequence/[@cycle='1']/Frame/PVStateShard/PVStateValue/[@key='positionCurrent']/SubindexedValues/[@index='ZAxis']/SubindexedValue/[@subindex='0']"
)
]
assert (
len(z_fields) == n_depths
), "Number of z fields does not match number of depths."
metainfo = dict(
num_fields=n_fields,
num_channels=n_channels,
num_planes=n_depths,
num_frames=n_frames,
num_rois=roi,
x_pos=None,
y_pos=None,
z_pos=None,
frame_rate=framerate,
bidirectional=bidirectional_scan,
bidirectional_z=bidirection_z,
scan_datetime=scan_datetime,
usecs_per_line=usec_per_line,
scan_duration=total_scan_duration,
height_in_pixels=pixel_height,
width_in_pixels=pixel_width,
height_in_um=um_height,
width_in_um=um_width,
fieldX=x_field,
fieldY=y_field,
fieldZ=z_fields,
recording_time=recording_start_time,
)
return metainfo
|