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format essnmx #209

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format essnmx #209

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20db897
formatESSNMX
aaronfinke Jan 16, 2025
b6b9364
Updated formatessnmx
aaronfinke Jan 20, 2025
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59 changes: 40 additions & 19 deletions src/dxtbx/format/FormatESSNMX.py
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Original file line number Diff line number Diff line change
Expand Up @@ -59,14 +59,12 @@ def get_experiment_description(self) -> str:
def _load_raw_data(self) -> None:
raw_data = []
image_size = self._get_image_size()
total_pixels = image_size[0] * image_size[1]
# total_pixels = image_size[0] * image_size[1]
num_images = self.get_num_images()
for i in range(self._get_num_panels()):
spectra = self._nxs_file["NMX_data"]["detector_1"]["counts"][
0, total_pixels * i : total_pixels * (i + 1), :
]
spectra = np.reshape(spectra, (image_size[0], image_size[1], num_images))
raw_data.append(flumpy.from_numpy(spectra))
spectra = self._nxs_file["NMX_data"]["detector_1"]["counts"][i, :, :]
spectra = np.reshape(spectra, (image_size, num_images))
raw_data.append(flumpy.from_numpy(np.ascontiguousarray(spectra)))

self._raw_data = tuple(raw_data)

Expand All @@ -75,7 +73,7 @@ def get_raw_data(
) -> Tuple[flex.int]:
raw_data = []
image_size = self._get_image_size()
total_pixels = image_size[0] * image_size[1]
# total_pixels = image_size[0] * image_size[1]

if use_loaded_data:
if self._raw_data is None:
Expand All @@ -88,8 +86,11 @@ def get_raw_data(

else:
for i in range(self._get_num_panels()):
# spectra = self._nxs_file["NMX_data"]["detector_1"]["counts"][
# 0, total_pixels * i : total_pixels * (i + 1), index : index + 1
# ]
spectra = self._nxs_file["NMX_data"]["detector_1"]["counts"][
0, total_pixels * i : total_pixels * (i + 1), index : index + 1
i, :, index
]
spectra = np.reshape(spectra, image_size)
raw_data.append(flumpy.from_numpy(np.ascontiguousarray(spectra)))
Expand All @@ -98,7 +99,10 @@ def get_raw_data(

def _get_time_channel_bins(self) -> List[float]:
# (usec)
return self._nxs_file["NMX_data"]["detector_1"]["t_bin"][:] * 10**6
if np.ndim(self._nxs_file["NMX_data"]["detector_1"]["t_bin"][:]) == 1:
return self._nxs_file["NMX_data"]["detector_1"]["t_bin"][:] * 10**6
else:
return self._nxs_file["NMX_data"]["detector_1"]["t_bin"][1] * 10**6

def _get_time_of_flight(self) -> List[float]:
# (usec)
Expand Down Expand Up @@ -130,7 +134,15 @@ def get_detector(self, index: int = None) -> Detector:
panel.set_image_size(image_size)
panel.set_trusted_range(trusted_range)
panel.set_pixel_size(pixel_size)
# old_origin = np.array(panel_origins[i])
# fast_axis = np.array(fast_axes[i])
# slow_axis = np.array(slow_axes[i])
# New_origin = tuple(old_origin + slow_axis* 0.4 * 1280 + fast_axis* 0.4 * 1280)
# fast_axis = tuple(fast_axis)
# slow_axis = tuple(slow_axis)
# panel.set_local_frame(fast_axis, slow_axis, New_origin)
panel.set_local_frame(fast_axes[i], slow_axes[i], panel_origins[i])

panel.set_gain(gain)
r, t = panel_projections[i]
r = tuple(map(int, r))
Expand All @@ -140,13 +152,11 @@ def get_detector(self, index: int = None) -> Detector:
return detector

def _get_num_panels(self) -> int:
return self._nxs_file["NMX_data/instrument"].attrs["nr_detector"]
num_rows = self._nxs_file["NMX_data"]["NXdetector"]["fast_axis"].shape
return num_rows[0]

def _get_panel_names(self) -> List[str]:
return [
"%02d" % (i + 1)
for i in range(self._nxs_file["NMX_data/instrument"].attrs["nr_detector"])
]
return ["%02d" % (i + 1) for i in range(self._get_num_panels())]

def _get_panel_type(self) -> str:
return "SENSOR_PAD"
Expand All @@ -164,14 +174,25 @@ def _get_pixel_size(self) -> Tuple[float, float]:
return (0.4, 0.4)

def _get_panel_fast_axes(self) -> Tuple[Tuple[float, float, float]]:
return ((1.0, 0.0, 0.0), (0.0, 0.0, 1.0), (0.0, 0.0, -1.0))
# return ((1.0, 0.0, 0.0), (0.0, 0.0, 1.0), (0.0, 0.0, -1.0))
fast_axes = self._nxs_file["NMX_data/NXdetector"]["fast_axis"][:]
return (tuple(fast_axes[0]), tuple(fast_axes[1]), tuple(fast_axes[2]))

def _get_panel_slow_axes(self) -> Tuple[Tuple[float, float, float]]:
return ((0.0, 1.0, 0.0), (0.0, 1.0, 0.0), (0.0, 1.0, 0.0))
# return ((0.0, 1.0, 0.0), (0.0, 1.0, 0.0), (0.0, 1.0, 0.0))
slow_axes = self._nxs_file["NMX_data/NXdetector"]["slow_axis"][:]
return (tuple(slow_axes[0]), tuple(slow_axes[1]), tuple(slow_axes[2]))

def _get_panel_origins(self) -> Tuple[Tuple[float, float, float]]:
# (mm)
return ((-250, -250.0, -292.0), (290, -250.0, -250), (-290, -250.0, 250.0))
# return ((-250, -250.0, -292.0), (290, -250.0, -250), (-290, -250.0, 250.0))

origin = self._nxs_file["NMX_data/NXdetector"]["origin"][:] * 1000
corrfact = np.array([[0, -256, -256], [-256.0, -256.0, 0], [0, -256, 256]])

corrorg = origin + corrfact
return (tuple(corrorg[0]), tuple(corrorg[1]), tuple(corrorg[2]))
# return (tuple(origin[0]),tuple(origin[1]),tuple(origin[2]))

def _get_panel_projections_2d(self) -> dict[int : Tuple[Tuple, Tuple]]:
p_w, p_h = self._get_image_size()
Expand All @@ -197,11 +218,11 @@ def get_beam(self, index: int = None) -> PolychromaticBeam:
)

def _get_sample_to_source_direction(self) -> Tuple[float, float, float]:
return (0, 0, 1)
return (0, 0, -1)

def _get_wavelength_range(self) -> Tuple[float, float]:
# (A)
return (1.8, 2.55)
return (1.8, 3.55)

def _get_sample_to_source_distance(self) -> float:
try:
Expand Down
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