import logging
from posixpath import join
import numpy as np
from tomoscan.esrf.scan.h5utils import get_h5_value
from nxtomo.application.nxtomo import NXtomo
from nxtomo.nxobject.nxdetector import ImageKey
from tomoscan.esrf.scan.fscan import FscanDataset, list_datasets
_logger = logging.getLogger(__name__)
[docs]def from_fscan_to_nx(
fname,
output_fname,
detector_name="pcoedgehs",
rotation_motor_name="hrrz",
halftomo=False,
ignore_last_n_projections=0,
energy=None,
distance=None,
):
entries = list_datasets(fname)
if len(entries) < 3:
_logger.error(
"Error: Expected at least three datasets, got only %d" % (len(entries))
)
return
do_360 = False
if len(entries) == 6:
# 360 degrees scans are done in two parts: [1.1, 2.1, 3.1] and then [4.1, 5.1]
do_360 = True
projs = FscanDataset(fname, detector_name=detector_name, entry="1.1")
flats = FscanDataset(fname, detector_name=detector_name, entry="2.1")
darks = FscanDataset(fname, detector_name=detector_name, entry="3.1")
if do_360:
projs2 = FscanDataset(fname, detector_name=detector_name, entry="4.1")
flats2 = FscanDataset(fname, detector_name=detector_name, entry="5.1")
# Some datasets don't have the 6.1 entry.
# Anyway nabu does not support several series of darks.
# For now it's safer to ignore the second series of darks
try:
darks2 = FscanDataset(fname, detector_name=detector_name, entry="6.1")
except ValueError:
_logger.error("Could not find entry 6.1, proceeding")
darks2 = None
if darks2 is not None:
_logger.warning(
"Discarding entry 6.1 as nabu does not support several series of darks yet"
)
my_nxtomo = NXtomo()
data_urls = [darks.dataset_hdf5_url, flats.dataset_hdf5_url, projs.dataset_hdf5_url]
if do_360:
data_urls.extend(
[
# darks2.dataset_hdf5_url,
flats2.dataset_hdf5_url,
projs2.dataset_hdf5_url,
]
)
my_nxtomo.instrument.detector.data = data_urls
img_keys = [
[ImageKey.DARK_FIELD] * darks.data_shape[0],
[ImageKey.FLAT_FIELD] * flats.data_shape[0],
[ImageKey.PROJECTION] * (projs.data_shape[0] - ignore_last_n_projections),
[ImageKey.ALIGNMENT] * ignore_last_n_projections,
]
if do_360:
img_keys.extend(
[
# [ImageKey.DARK_FIELD] * darks2.data_shape[0],
[ImageKey.FLAT_FIELD] * flats2.data_shape[0],
[ImageKey.PROJECTION]
* (projs2.data_shape[0] - ignore_last_n_projections),
[ImageKey.ALIGNMENT] * ignore_last_n_projections,
]
)
my_nxtomo.instrument.detector.image_key_control = np.concatenate(img_keys)
rotation_angles_path = join(projs.entry, f"instrument/{rotation_motor_name}/data")
rotation_angles = get_h5_value(projs.fname, rotation_angles_path)
# Sometimes values are in /data, sometimes in /value ... who needs a stable format anyway ?
if rotation_angles is None:
_logger.error(
f"Could not find the rotation angles in {rotation_angles_path}, trying in /values"
)
rotation_angles_path = rotation_angles_path.replace("/data", "/value")
# ---
rotation_angles = get_h5_value(projs.fname, rotation_angles_path)
if rotation_angles is not None:
last_idx = None
if ignore_last_n_projections > 0:
last_idx = -ignore_last_n_projections
rotation_angles = [
[0] * darks.data_shape[0],
[0] * flats.data_shape[0],
rotation_angles[:last_idx],
[0] * ignore_last_n_projections,
]
if do_360:
rotation_angles2 = get_h5_value(
projs2.fname,
join(projs2.entry, f"instrument/{rotation_motor_name}/data"),
)
rotation_angles.extend(
[
# [0] * darks2.data_shape[0],
[0] * flats2.data_shape[0],
rotation_angles2[:last_idx],
[0] * ignore_last_n_projections,
]
)
my_nxtomo.sample.rotation_angle = np.concatenate(rotation_angles)
my_nxtomo.instrument.detector.field_of_view = (
"Half" if (halftomo and do_360) else "Full"
)
my_nxtomo.instrument.detector.x_pixel_size = (
my_nxtomo.instrument.detector.y_pixel_size
) = (6.5 * 1e-6)
if energy is not None:
my_nxtomo.energy = energy # in keV by default
if distance is not None:
my_nxtomo.instrument.detector.distance = distance # in meter
my_nxtomo.save(
file_path=output_fname,
data_path="entry",
overwrite=True,
nexus_path_version=1.1,
)
