Extract metadata for scans generated by PrairieView acquisition software.
The PrairieView software generates one .ome.tif imaging file per frame acquired. The
metadata for all frames is contained one .xml file. This function locates the .xml
file and generates a dictionary necessary to populate the DataJoint ScanInfo and
Field tables. PrairieView works with resonance scanners with a single field.
PrairieView does not support bidirectional x and y scanning. ROI information is not
contained in the .xml file. All images generated using PrairieView have square
dimensions(e.g. 512x512).
Parameters:
| Name |
Type |
Description |
Default |
pvtiffile |
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 pvtiffile. |
Returns:
| Name | Type |
Description |
metainfo |
dict
|
A dict mapping keys to corresponding metadata values fetched from the
.xml file. |
Source code in element_interface/prairieviewreader.py
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190 | def get_pv_metadata(pvtiffile: str) -> dict:
"""Extract metadata for scans generated by PrairieView acquisition software.
The PrairieView software generates one .ome.tif imaging file per frame acquired. The
metadata for all frames is contained one .xml file. This function locates the .xml
file and generates a dictionary necessary to populate the DataJoint ScanInfo and
Field tables. PrairieView works with resonance scanners with a single field.
PrairieView does not support bidirectional x and y scanning. ROI information is not
contained in the .xml file. All images generated using PrairieView have square
dimensions(e.g. 512x512).
Args:
pvtiffile: 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 `pvtiffile`.
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 = pathlib.Path(pvtiffile).parent.glob("*.xml")
for xml_file in xml_files:
tree = ET.parse(xml_file)
root = tree.getroot()
if root.find(".//Sequence"):
break
else:
raise FileNotFoundError(
f"No PrarieView metadata XML file found at {pvtiffile.parent}"
)
bidirectional_scan = False # Does not support bidirectional
roi = 0
n_fields = 1 # Always contains 1 field
record_start_time = root.find(".//Sequence/[@cycle='1']").attrib.get("time")
# Get all channels and find unique values
channel_list = [
int(channel.attrib.get("channel"))
for channel in root.iterfind(".//Sequence/Frame/File/[@channel]")
]
n_channels = len(set(channel_list))
n_frames = len(root.findall(".//Sequence/Frame"))
framerate = 1 / float(
root.findall('.//PVStateValue/[@key="framePeriod"]')[0].attrib.get("value")
) # rate = 1/framePeriod
usec_per_line = (
float(
root.findall(".//PVStateValue/[@key='scanLinePeriod']")[0].attrib.get(
"value"
)
)
* 1e6
) # Convert from seconds to microseconds
scan_datetime = datetime.strptime(root.attrib.get("date"), "%m/%d/%Y %I:%M:%S %p")
total_duration = float(
root.findall(".//Sequence/Frame")[-1].attrib.get("relativeTime")
)
px_height = int(
root.findall(".//PVStateValue/[@key='pixelsPerLine']")[0].attrib.get("value")
)
# All PrairieView-acquired images have square dimensions (512 x 512; 1024 x 1024)
px_width = px_height
um_per_pixel = float(
root.find(
".//PVStateValue/[@key='micronsPerPixel']/IndexedValue/[@index='XAxis']"
).attrib.get("value")
)
um_height = um_width = float(px_height) * um_per_pixel
# x and y coordinate values for the center of the field
x_field = float(
root.find(
".//PVStateValue/[@key='currentScanCenter']/IndexedValue/[@index='XAxis']"
).attrib.get("value")
)
y_field = float(
root.find(
".//PVStateValue/[@key='currentScanCenter']/IndexedValue/[@index='YAxis']"
).attrib.get("value")
)
if (
root.find(
".//Sequence/[@cycle='1']/Frame/PVStateShard/PVStateValue/[@key='positionCurrent']/SubindexedValues/[@index='ZAxis']"
)
is None
):
z_fields = np.float64(
root.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 = root.find(".//Sequence").attrib.get("bidirectionalZ") == "True"
# One "Frame" per depth. Gets number of frames in first sequence
planes = [
int(plane.attrib.get("index"))
for plane in root.findall(".//Sequence/[@cycle='1']/Frame")
]
n_depths = len(set(planes))
z_controllers = root.findall(
".//Sequence/[@cycle='1']/Frame/[@index='1']/PVStateShard/PVStateValue/[@key='positionCurrent']/SubindexedValues/[@index='ZAxis']/SubindexedValue"
)
if len(z_controllers) > 1:
z_repeats = []
for controller in root.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 root.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 root.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_duration,
height_in_pixels=px_height,
width_in_pixels=px_width,
height_in_um=um_height,
width_in_um=um_width,
fieldX=x_field,
fieldY=y_field,
fieldZ=z_fields,
recording_time=record_start_time,
)
return metainfo
|