-
Notifications
You must be signed in to change notification settings - Fork 18
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Add format class to understand Jungfrau4M serial data from ID29, ESRF
- Loading branch information
1 parent
9657a16
commit 7d4f95b
Showing
2 changed files
with
164 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1 @@ | ||
Add format class to read Jungfrau4M serial images from beamline ID29 at ESRF |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,163 @@ | ||
from __future__ import annotations | ||
|
||
import sys | ||
|
||
import h5py | ||
|
||
from scitbx.array_family import flex | ||
|
||
from dxtbx import flumpy | ||
from dxtbx.format.FormatHDF5 import FormatHDF5 | ||
|
||
|
||
class FormatHDF5ESRFJungfrau4M(FormatHDF5): | ||
|
||
# A class to understand still-shot images from ESRF collected on a Jungfrau 4M. | ||
|
||
_cached_mask = None | ||
|
||
@staticmethod | ||
def understand(image_file): | ||
with h5py.File(image_file, "r") as h5_handle: | ||
if len(h5_handle) != 1: | ||
return False | ||
key = list(h5_handle.keys())[0] | ||
if "instrument" not in h5_handle[key]: | ||
return False | ||
if "jungfrau4m_rr_smx" not in h5_handle[key]["instrument"]: | ||
return False | ||
return True | ||
|
||
def _start(self): | ||
super()._start() | ||
image_file = self.get_image_file() | ||
self._h5_handle = h5py.File(image_file, "r") | ||
self.key = list(self._h5_handle.keys())[0] | ||
self.n_images = self._h5_handle[self.key]["instrument"]["jungfrau4m_rr_smx"][ | ||
"data" | ||
].shape[0] | ||
self.adus_per_photon = self._h5_handle[self.key]["instrument"][ | ||
"jungfrau4m_rr_smx" | ||
]["detector_information"]["adus_per_photon"] | ||
self.image_size = tuple( | ||
self._h5_handle[self.key]["instrument"]["jungfrau4m_rr_smx"]["data"].shape[ | ||
1: | ||
] | ||
) | ||
wavelength = self._h5_handle[self.key]["instrument"]["jungfrau4m_rr_smx"][ | ||
"beam" | ||
]["incident_wavelength"][()] | ||
x_pixel_size = ( | ||
self._h5_handle[self.key]["instrument"]["jungfrau4m_rr_smx"][ | ||
"detector_information" | ||
]["x_pixel_size"][()] | ||
* 1000 | ||
) # convert m to mm | ||
y_pixel_size = ( | ||
self._h5_handle[self.key]["instrument"]["jungfrau4m_rr_smx"][ | ||
"detector_information" | ||
]["y_pixel_size"][()] | ||
* 1000 | ||
) # convert m to mm | ||
distance = ( | ||
self._h5_handle[self.key]["instrument"]["jungfrau4m_rr_smx"][ | ||
"detector_information" | ||
]["detector_distance"][()] | ||
* 1000 | ||
) # convert m to mm | ||
beam_center_x = self._h5_handle[self.key]["instrument"]["jungfrau4m_rr_smx"][ | ||
"detector_information" | ||
]["beam_center_x"][ | ||
() | ||
] # in px | ||
beam_center_y = self._h5_handle[self.key]["instrument"]["jungfrau4m_rr_smx"][ | ||
"detector_information" | ||
]["beam_center_y"][ | ||
() | ||
] # in px | ||
|
||
beam_center_x *= x_pixel_size | ||
beam_center_y *= y_pixel_size | ||
trusted_range = ( | ||
self._h5_handle[self.key]["instrument"]["jungfrau4m_rr_smx"][ | ||
"detector_information" | ||
]["underload_value"][()], | ||
self._h5_handle[self.key]["instrument"]["jungfrau4m_rr_smx"][ | ||
"detector_information" | ||
]["saturation_value"][()], | ||
) | ||
exposure_time = self._h5_handle[self.key]["instrument"]["jungfrau4m_rr_smx"][ | ||
"acquisition" | ||
]["exposure_time"][()] | ||
|
||
self._detector_model = self._detector_factory.simple( | ||
sensor="UNKNOWN", | ||
distance=distance, | ||
beam_centre=( | ||
beam_center_x, | ||
beam_center_y, | ||
), | ||
fast_direction="+x", | ||
slow_direction="-y", | ||
pixel_size=( | ||
x_pixel_size, | ||
y_pixel_size, | ||
), | ||
image_size=(self.image_size[1], self.image_size[0]), | ||
trusted_range=trusted_range, | ||
mask=self.get_static_mask(), | ||
) | ||
self._beam_model = self._beam_factory.simple(wavelength) | ||
self._scan_model = self._scan_factory.make_scan( | ||
image_range=(1, self.n_images), | ||
exposure_times=exposure_time, | ||
oscillation=(0.0, 0.0), | ||
epochs=list(range(self.n_images)), | ||
) | ||
self._goniometer_model = self._goniometer_factory.known_axis((0, 1, 0)) | ||
|
||
def get_raw_data(self, index=None): | ||
if index is None: | ||
index = 0 | ||
|
||
data = ( | ||
self._h5_handle[self.key]["measurement"]["data"][index] | ||
/ self.adus_per_photon | ||
) | ||
return flex.double(data.astype(float)) | ||
|
||
def get_num_images(self): | ||
return self.n_images | ||
|
||
def get_beam(self, index=None): | ||
return self._beam(index) | ||
|
||
def _beam(self, index=None): | ||
return self._beam_model | ||
|
||
def get_detector(self, index=None): | ||
return self._detector(index) | ||
|
||
def get_static_mask(self): | ||
if FormatHDF5ESRFJungfrau4M._cached_mask is None: | ||
mask = self._h5_handle[self.key]["instrument"]["jungfrau4m_rr_smx"][ | ||
"detector_information" | ||
]["pixel_mask"] | ||
mask = flumpy.from_numpy(mask[()]) | ||
mask_array = mask == 0 | ||
FormatHDF5ESRFJungfrau4M._cached_mask = mask_array | ||
return FormatHDF5ESRFJungfrau4M._cached_mask | ||
|
||
def _detector(self, index=None): | ||
return self._detector_model | ||
|
||
def _goniometer(self): | ||
return self._goniometer_model | ||
|
||
def _scan(self): | ||
return self._scan_model | ||
|
||
|
||
if __name__ == "__main__": | ||
for arg in sys.argv[1:]: | ||
print(FormatHDF5ESRFJungfrau4M.understand(arg)) |