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Update CL metadata in dm-reader #2894

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merged 10 commits into from Mar 15, 2022
Merged

Update CL metadata in dm-reader #2894

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015493c
update cl metadata
jlaehne Feb 23, 2022
8ae6102
Integrate Monarc Metadata
jlaehne Feb 28, 2022
ab1754f
Monarc tests
jlaehne Mar 1, 2022
69da5a6
Merge remote-tracking branch 'upstream/RELEASE_next_minor' into dm_cl…
jlaehne Mar 1, 2022
66e53d6
fix Monarc tests
jlaehne Mar 1, 2022
ebb7a3c
update release info
jlaehne Mar 3, 2022
f6e7fa1
update pixel-size
jlaehne Mar 3, 2022
6660bf0
update pixel_size
jlaehne Mar 10, 2022
9fd4a80
review ericpre
jlaehne Mar 14, 2022
1503b9f
increase coverage
jlaehne Mar 14, 2022
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115 changes: 81 additions & 34 deletions hyperspy/io_plugins/digital_micrograph.py
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Expand Up @@ -858,6 +858,25 @@ def _get_EELS_exposure_time(self, tags):
else:
_logger.info("EELS exposure time can't be read.")

def _get_CL_detector_type(self, tags):
if "Acquisition_Mode" in tags and tags["Acquisition_Mode"] == "Parallel dispersive":
return "CCD"
elif "Acquisition_Mode" in tags and tags["Acquisition_Mode"] == "Serial dispersive":
return "PMT"
else:
_logger.info("CL detector type can't be read.")

def _get_CL_exposure_time(self, tags):
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if 'Integration_time_s' in tags:
return float(tags["Integration_time_s"])
elif 'Exposure_s' in tags:
frame_number = 1
if "Number_of_frames" in tags:
frame_number = float(tags["Number_of_frames"])
return float(tags["Exposure_s"]) * frame_number
else:
_logger.info("CL exposure time can't be read.")

def get_mapping(self):
if 'source' in self.imdict.ImageTags.keys():
# For stack created with the stack builder plugin
Expand All @@ -868,27 +887,32 @@ def get_mapping(self):
tags_path = 'ImageList.TagGroup0.ImageTags'
image_tags_dict = self.imdict.ImageTags
is_scanning = "DigiScan" in image_tags_dict.keys()
# check if instrument is SEM or TEM
if "Microscope Info" in self.imdict.ImageTags and "Illumination Mode" in self.imdict.ImageTags["Microscope Info"]:
microscope = "SEM" if self._get_mode(self.imdict.ImageTags["Microscope Info"]["Illumination Mode"]) == "SEM" else "TEM"
else:
microscope = "TEM"
mapping = {
"{}.DataBar.Acquisition Date".format(tags_path): (
"General.date", self._get_date),
"{}.DataBar.Acquisition Time".format(tags_path): (
"General.time", self._get_time),
"{}.Microscope Info.Voltage".format(tags_path): (
"Acquisition_instrument.TEM.beam_energy", lambda x: x / 1e3),
"Acquisition_instrument.%s.beam_energy" % microscope, lambda x: x / 1e3),
"{}.Microscope Info.Stage Position.Stage Alpha".format(tags_path): (
"Acquisition_instrument.TEM.Stage.tilt_alpha", None),
"Acquisition_instrument.%s.Stage.tilt_alpha" % microscope, None),
"{}.Microscope Info.Stage Position.Stage Beta".format(tags_path): (
"Acquisition_instrument.TEM.Stage.tilt_beta", None),
"Acquisition_instrument.%s.Stage.tilt_beta" % microscope, None),
"{}.Microscope Info.Stage Position.Stage X".format(tags_path): (
"Acquisition_instrument.TEM.Stage.x", lambda x: x * 1e-3),
"Acquisition_instrument.%s.Stage.x" % microscope, lambda x: x * 1e-3),
"{}.Microscope Info.Stage Position.Stage Y".format(tags_path): (
"Acquisition_instrument.TEM.Stage.y", lambda x: x * 1e-3),
"Acquisition_instrument.%s.Stage.y" % microscope, lambda x: x * 1e-3),
"{}.Microscope Info.Stage Position.Stage Z".format(tags_path): (
"Acquisition_instrument.TEM.Stage.z", lambda x: x * 1e-3),
"Acquisition_instrument.%s.Stage.z" % microscope, lambda x: x * 1e-3),
"{}.Microscope Info.Illumination Mode".format(tags_path): (
"Acquisition_instrument.TEM.acquisition_mode", self._get_mode),
"Acquisition_instrument.%s.acquisition_mode" % microscope, self._get_mode),
"{}.Microscope Info.Probe Current (nA)".format(tags_path): (
"Acquisition_instrument.TEM.beam_current", None),
"Acquisition_instrument.%s.beam_current" % microscope, None),
"{}.Session Info.Operator".format(tags_path): (
"General.authors", self._parse_string),
"{}.Session Info.Specimen".format(tags_path): (
Expand Down Expand Up @@ -921,16 +945,16 @@ def get_mapping(self):
else:
mapping.update({
"{}.Microscope Info.STEM Camera Length".format(tags_path): (
"Acquisition_instrument.TEM.camera_length",
"Acquisition_instrument.%s.camera_length" % microscope,
None),
"{}.Microscope Info.Indicated Magnification".format(tags_path): (
"Acquisition_instrument.TEM.magnification",
"Acquisition_instrument.%s.magnification" % microscope,
None),
})

mapping.update({
tags_path: (
"Acquisition_instrument.TEM.microscope",
"Acquisition_instrument.%s.microscope" % microscope,
self._get_microscope_name),
})
if "SI" in self.imdict.ImageTags.keys():
Expand Down Expand Up @@ -1001,59 +1025,82 @@ def get_mapping(self):
"Acquisition_instrument.TEM.Detector.EDS.real_time",
None),
})
elif self.signal_type == "CL":
elif self.signal_type == "CL" or ("Acquisition" in image_tags_dict.keys() and "Monarc_Spectrometer" in image_tags_dict["Acquisition"].keys()):
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mapping.update({
"{}.CL.Acquisition.Date".format(tags_path): (
"General.date", self._get_date),
"{}.CL.Acquisition.Start_time".format(tags_path): (
"General.time", self._get_time),
"{}.Meta_Data.Acquisition_Mode".format(tags_path): (
"Acquisition_instrument.CL.acquisition_mode", None),
"Acquisition_instrument.Spectrometer.acquisition_mode", None),
"{}.Meta_Data.Format".format(tags_path): (
"Signal.format", None),
"{}.Meta_Data".format(tags_path): (
"Acquisition_instrument.Detector.detector_type",
self._get_CL_detector_type),
"{}.Acquisition.Monarc_Spectrometer.Grating".format(tags_path): (
"Acquisition_instrument.Spectrometer.Grating.groove_density",
lambda string: self._parse_string(string,
convert_to_float=True,
tag_name='Grating')),
"{}.CL.Acquisition.Dispersion_grating_(lines/mm)".format(tags_path): (
"Acquisition_instrument.CL.dispersion_grating", None),
"Acquisition_instrument.Spectrometer.Grating.groove_density", None),
"{}.Acquisition.Monarc_Spectrometer.Slit_Width".format(tags_path): (
"Acquisition_instrument.Spectrometer.entrance_slit_width", None),
"{}.Acquisition.Monarc_Spectrometer.Bandpass".format(tags_path): (
"Acquisition_instrument.Spectrometer.bandpass", None),
# Parallel spectrum
"{}.CL.Acquisition.Central_wavelength_(nm)".format(tags_path): (
"Acquisition_instrument.CL.central_wavelength", None),
"Acquisition_instrument.Spectrometer.central_wavelength", None),
"{}.CL.Acquisition.Exposure_(s)".format(tags_path): (
"Acquisition_instrument.CL.exposure", None),
"Acquisition_instrument.Detector.exposure_per_frame", None),
"{}.CL.Acquisition.Number_of_frames".format(tags_path): (
"Acquisition_instrument.CL.frame_number", None),
"{}.CL.Acquisition.Integration_time_(s)".format(tags_path): (
"Acquisition_instrument.CL.integration_time", None),
"Acquisition_instrument.Detector.frames", None),
"{}.CL.Acquisition".format(tags_path): (
"Acquisition_instrument.Detector.integration_time",
self._get_CL_exposure_time),
"{}.CL.Acquisition.Saturation_fraction".format(tags_path): (
"Acquisition_instrument.CL.saturation_fraction", None),
"Acquisition_instrument.Detector.saturation_fraction", None),
"{}.Acquisition.Parameters.High_Level.Binning".format(tags_path): (
"Acquisition_instrument.CL.CCD.binning", None),
"Acquisition_instrument.Detector.binning", None),
"{}.Acquisition.Parameters.High_Level.CCD_Read_Area".format(tags_path): (
"Acquisition_instrument.CL.CCD.read_area", None),
"Acquisition_instrument.Detector.sensor_roi", None),
"{}.Acquisition.Parameters.High_Level.Processing".format(tags_path): (
"Acquisition_instrument.CL.CCD.processing", None),
"Acquisition_instrument.Detector.processing", None),
"{}.Acquisition.Device.CCD.Pixel_Size_um".format(tags_path): (
"Acquisition_instrument.Detector.pixel_size",
lambda x: x[0] if (isinstance(x, tuple) and x[0] == x[1]) else x),
# Serial Spectrum
"{}.CL.Acquisition.Acquisition_begin".format(tags_path): (
"General.date", self._get_date),
"{}.CL.Acquisition.Detector_type".format(tags_path): (
"Acquisition_instrument.CL.detector_type", None),
"{}.CL.Acquisition.Dwell_time_(s)".format(tags_path): (
"Acquisition_instrument.CL.dwell_time", None),
"Acquisition_instrument.Detector.integration_time", None),
"{}.CL.Acquisition.Start_wavelength_(nm)".format(tags_path): (
"Acquisition_instrument.CL.start_wavelength", None),
"Acquisition_instrument.Spectrometer.start_wavelength", None),
"{}.CL.Acquisition.Step-size_(nm)".format(tags_path): (
"Acquisition_instrument.CL.step_size", None),
"Acquisition_instrument.Spectrometer.step_size", None),
# PMT image
"{}.Acquisition.Monarc_Spectrometer.PMT_HV".format(tags_path): (
"Acquisition_instrument.Detector.pmt_voltage", None),
"{}.DigiScan.Sample Time".format(tags_path): (
"Acquisition_instrument.%s.dwell_time" % microscope,
lambda x: x / 1e6),
# SI
"{}.DataBar.Acquisition_Date".format(tags_path): (
"General.date", self._get_date),
"{}.DataBar.Acquisition_Time".format(tags_path): (
"General.time", self._get_time),
"{}.SI.Acquisition.SI_Application_Mode.Name".format(tags_path): (
"Acquisition_instrument.Spectrum_image.mode", None),
"{}.SI.Acquisition.Artefact_Correction.Spatial_Drift.Periodicity".format(tags_path): (
"Acquisition_instrument.CL.SI.drift_correction_periodicity", None),
"Acquisition_instrument.Spectrum_image.drift_correction_periodicity", None),
"{}.SI.Acquisition.Artefact_Correction.Spatial_Drift.Units".format(tags_path): (
"Acquisition_instrument.CL.SI.drift_correction_units", None),
"{}.SI.Acquisition.SI_Application_Mode.Name".format(tags_path): (
"Acquisition_instrument.CL.SI.mode", None),

"Acquisition_instrument.Spectrum_image.drift_correction_units", None),
})
elif "DigiScan" in image_tags_dict.keys():
mapping.update({
"{}.DigiScan.Sample Time".format(tags_path): (
"Acquisition_instrument.TEM.dwell_time",
"Acquisition_instrument.%s.dwell_time" % microscope,
lambda x: x / 1e6),
})
else:
Expand Down
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0 ...s/io/dm4_1D_data/test-CL_spectrum-pmt.dm4 → .../dm4_1D_data/test-MonoCL_spectrum-pmt.dm4
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