Per shot wavelength, second try #717
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-Specify how to do monochromatic shot-to-shot variation -Specify how to do polychromatic shot-to-shot variation -Include shot-to-shot variation in wacelength spread
- Remove TODO - detector element -> detector module. - Typos - Extend flux and total_flux to allow shot-to-shot variation - Remove non-required items from NXSource and reference that they can be found in the base class documentation Thanks @benajamin, @yayahjb, @PeterC-DLS, @prjemian for the review. Yay code camp!
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This fixes #696 |
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SpectrumBeam has these methods: set_spectrum(flex.double energies, flex.double weights) get_spectrum_energies() get_spectrum_weights() get_weighted_wavelength() Two flex arrays, energies (eV) and weights (dimensionless), represent the spectrum as a scatter plot. This follows the conventions set up in nexusformat/definitions#717. The new function get_weighted_wavelength uses a simple weighted mean to determine a wavelength. It is ok if the SpectrumBeam has a wavelength != get_weighted_wavelength. This represents a calibrated wavelength determined from processing the spectrum. is_similar_to tests get_weighted_wavelength between the two beams. Includes tests.
phyy-nx
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Apr 3, 2020
Uses the unofficial key incident_wavelength_calculated, but otherwise implements nexusformat/definitions#717.
phyy-nx
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Apr 3, 2020
Uses the convention of nexusformat/definitions#717 with the addition of a yet-unofficial field, incident_wavelength_calculated, to store the calculated wavelength SwissFEL provides. This wavelength comes from a smoothed, fitted processing of the spectra. As it can be considered derived information, so is in a separate dataset.
phyy-nx
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Apr 3, 2020
Uses the unofficial key incident_wavelength_calculated, but otherwise implements nexusformat/definitions#717.
phyy-nx
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to cctbx/dxtbx
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Apr 8, 2020
Adds these methods: set_spectrum(flex.double energies, flex.double weights) get_spectrum_energies() get_spectrum_weights() get_weighted_wavelength() Two flex arrays, energies (eV) and weights (dimensionless), represent the spectrum as a scatter plot. This follows the conventions set up in nexusformat/definitions#717. The new function get_weighted_wavelength uses a simple weighted mean to determine a wavelength. It is ok if the beam has a wavelength != get_weighted_wavelength. This represents a calibrated wavelength determined from processing the spectrum. is_similar_to tests get_weighted_wavelength between the two beams, if a spectrum is present. Includes tests.
phyy-nx
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Apr 9, 2020
Adds these methods: set_spectrum(flex.double energies, flex.double weights) get_spectrum_energies() get_spectrum_weights() get_weighted_wavelength() Two flex arrays, energies (eV) and weights (dimensionless), represent the spectrum as a scatter plot. This follows the conventions set up in nexusformat/definitions#717. The new function get_weighted_wavelength uses a simple weighted mean to determine a wavelength. It is ok if the beam has a wavelength != get_weighted_wavelength. This represents a calibrated wavelength determined from processing the spectrum. is_similar_to tests get_weighted_wavelength between the two beams, if a spectrum is present. Includes tests.
phyy-nx
added a commit
to cctbx/dxtbx
that referenced
this pull request
Apr 9, 2020
Uses the unofficial key incident_wavelength_calculated, but otherwise implements nexusformat/definitions#717
phyy-nx
added a commit
to cctbx/dxtbx
that referenced
this pull request
Apr 9, 2020
Adds these methods: set_spectrum(flex.double energies, flex.double weights) get_spectrum_energies() get_spectrum_weights() get_weighted_wavelength() Two flex arrays, energies (eV) and weights (dimensionless), represent the spectrum as a scatter plot. This follows the conventions set up in nexusformat/definitions#717. The new function get_weighted_wavelength uses a simple weighted mean to determine a wavelength. It is ok if the beam has a wavelength != get_weighted_wavelength. This represents a calibrated wavelength determined from processing the spectrum. is_similar_to tests get_weighted_wavelength between the two beams, if a spectrum is present. Includes tests.
phyy-nx
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Apr 14, 2020
Uses the convention of nexusformat/definitions#717 with the addition of a yet-unofficial field, incident_wavelength_calculated, to store the calculated wavelength SwissFEL provides. This wavelength comes from a smoothed, fitted processing of the spectra. As it can be considered derived information, so is in a separate dataset.
phyy-nx
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Apr 15, 2020
Uses the convention of nexusformat/definitions#717 with the addition of a yet-unofficial field, incident_wavelength_calculated, to store the calculated wavelength SwissFEL provides. This wavelength comes from a smoothed, fitted processing of the spectra. As it can be considered derived information, so is in a separate dataset.
phyy-nx
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that referenced
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May 4, 2020
Adds these methods: set_spectrum(flex.double energies, flex.double weights) get_spectrum_energies() get_spectrum_weights() get_weighted_wavelength() Two flex arrays, energies (eV) and weights (dimensionless), represent the spectrum as a scatter plot. This follows the conventions set up in nexusformat/definitions#717. The new function get_weighted_wavelength uses a simple weighted mean to determine a wavelength. It is ok if the beam has a wavelength != get_weighted_wavelength. This represents a calibrated wavelength determined from processing the spectrum. is_similar_to tests get_weighted_wavelength between the two beams, if a spectrum is present. Includes tests.
phyy-nx
added a commit
to cctbx/cctbx_project
that referenced
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May 5, 2020
Uses the convention of nexusformat/definitions#717 with the addition of a yet-unofficial field, incident_wavelength_calculated, to store the calculated wavelength SwissFEL provides. This wavelength comes from a smoothed, fitted processing of the spectra. As it can be considered derived information, so is in a separate dataset.
phyy-nx
added a commit
to cctbx/dxtbx
that referenced
this pull request
May 5, 2020
Uses the unofficial key incident_wavelength_calculated, but otherwise implements nexusformat/definitions#717
phyy-nx
added a commit
to cctbx/cctbx_project
that referenced
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May 12, 2020
Uses the convention of nexusformat/definitions#717 with the addition of a yet-unofficial field, incident_wavelength_calculated, to store the calculated wavelength SwissFEL provides. This wavelength comes from a smoothed, fitted processing of the spectra. As it can be considered derived information, so is in a separate dataset.
phyy-nx
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May 19, 2020
Uses the unofficial key incident_wavelength_calculated, but otherwise implements nexusformat/definitions#717
phyy-nx
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to cctbx/dxtbx
that referenced
this pull request
May 21, 2020
Uses the unofficial key incident_wavelength_calculated, but otherwise implements nexusformat/definitions#717
phyy-nx
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to cctbx/dxtbx
that referenced
this pull request
May 28, 2020
Adds these methods: set_spectrum(flex.double energies, flex.double weights) get_spectrum_energies() get_spectrum_weights() get_weighted_wavelength() Two flex arrays, energies (eV) and weights (dimensionless), represent the spectrum as a scatter plot. This follows the conventions set up in nexusformat/definitions#717. The new function get_weighted_wavelength uses a simple weighted mean to determine a wavelength. It is ok if the beam has a wavelength != get_weighted_wavelength. This represents a calibrated wavelength determined from processing the spectrum. is_similar_to tests get_weighted_wavelength between the two beams, if a spectrum is present. Includes tests.
phyy-nx
added a commit
to cctbx/dxtbx
that referenced
this pull request
May 28, 2020
Uses the unofficial key incident_wavelength_calculated, but otherwise implements nexusformat/definitions#717
phyy-nx
added a commit
to cctbx/dxtbx
that referenced
this pull request
May 29, 2020
Adds these methods: set_spectrum(flex.double energies, flex.double weights) get_spectrum_energies() get_spectrum_weights() get_weighted_wavelength() Two flex arrays, energies (eV) and weights (dimensionless), represent the spectrum as a scatter plot. This follows the conventions set up in nexusformat/definitions#717. The new function get_weighted_wavelength uses a simple weighted mean to determine a wavelength. It is ok if the beam has a wavelength != get_weighted_wavelength. This represents a calibrated wavelength determined from processing the spectrum. is_similar_to tests get_weighted_wavelength between the two beams, if a spectrum is present. Includes tests.
phyy-nx
added a commit
to cctbx/dxtbx
that referenced
this pull request
May 29, 2020
Uses the unofficial key incident_wavelength_calculated, but otherwise implements nexusformat/definitions#717
phyy-nx
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Jul 27, 2020
Details: - Add Spectrum C++ object that implements methods get_energies (eV), get_weights (unitless), and get_weighted_wavelenth (angstroms). Spectrum can only be set from constructor. - Add get_spectrum method to Format and FormatMultiImage - Add get_spectrum method to ImageSet. Does not cache it like it does for detector, beam, etc. - Implement get_spectrum in NeXus. Specifically implements nexusformat/definitions#717, using optional variants to specify a calibrated wavelength and a spectrum.
This was referenced Jul 27, 2020
phyy-nx
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Jul 29, 2020
* Add Spectrum as a read-only class obtainable from an imageset Details: - Add Spectrum C++ object that implements methods get_energies_eV (eV), get_weights (unitless), and get_weighted_wavelenth (angstroms). Spectrum can only be set from constructor. - Add get_spectrum method to Format and FormatMultiImage - Add get_spectrum method to ImageSet. Does not cache it like it does for detector, beam, etc. - Implement get_spectrum in NeXus. Specifically implements nexusformat/definitions#717, using optional variants to specify a calibrated wavelength and a spectrum. - Add test for c++ spectrum object - Add bandwidth calculation. Computes: emin_ev = 1% on CDF and emax_ev = 99% on CDF so 98% or more of the spectrum is within the range. Added a test for this, which has a computed approximation to a real SwissFEL spectrum (so could be useful in other tests) - Add weighted energy variance. Recover the weighted variance around the weighted mean. Add test which makes a clean Gaussian and recovers the same parameters. Co-authored-by: Graeme Winter <graeme.winter@gmail.com>
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Extend incident_wavelength to allow per-shot variation
Also, py2 bug in nxdl2rst.py.
Fixes #667