Polarisation efficiency correction #510

ohcpaull · 2020-11-01T22:55:13Z

First attempt at integrating polarised neutron reflectometry files in the reduction workflow. I have slightly altered the reduction code by adding some flags so it knows when data is polarised and to use the new dict element "m_spec_polcorr" instead of "m_spec" for polarised data. Let me know whether you're OK with this approach. I haven't implemented uncertainty analysis for the correction process yet.

-correct_PA_efficiencies applies the matrix equation to the raw data. -polarised_correction returns PlatypusNexus files that have a m_spec_polcorr attribute containing the efficiency corrected spectra -Have included an extra ReductionOption "polarised" which is True or False Still some minor teething issues that need to be ironed out

Needed to mess around with ReductionOptions to tell refnx when to reduce m_spec and when to reduce m_spec_polcorr. Still not 100% sure whether this is foolproof, but I am able to plot both raw and polarisation-corrected data using this. Need to make more robust for less vanilla test cases. Also included new functions in __init__ file

Include a processing step in polarised_correction, and added some comments

np.matrix will be deprecated eventually.

-correct_PA_efficiencies applies the matrix equation to the raw data. -polarised_correction returns PlatypusNexus files that have a m_spec_polcorr attribute containing the efficiency corrected spectra -Have included an extra ReductionOption "polarised" which is True or False Still some minor teething issues that need to be ironed out

Needed to mess around with ReductionOptions to tell refnx when to reduce m_spec and when to reduce m_spec_polcorr. Still not 100% sure whether this is foolproof, but I am able to plot both raw and polarisation-corrected data using this. Need to make more robust for less vanilla test cases. Also included new functions in __init__ file

Include a processing step in polarised_correction, and added some comments

np.matrix will be deprecated eventually.

andyfaff · 2020-12-02T01:18:33Z

refnx/reduce/platypusnexus.py

+        # If polarised, add an entry for the polarisation
+        # efficiency corrected spectra
+        if polarised is True:
+            d["m_spec_polcorr"] = np.zeros_like(m_spec)


How about d["m_spec_polcorr"] = None?

I don't think one needs the logic check either.

andyfaff · 2020-12-02T01:19:31Z

refnx/reduce/reduce.py

        """
+        # Ensure 'polarised' reduction option is initialized
+        if "polarised" not in reduction_options:
+            reduction_options["polarised"] = False


Do we need to check this? Just assume that polarised is in reduction_options.

andyfaff · 2020-12-02T01:23:37Z

refnx/reduce/platypusnexus.py

        normalise_bins=True,
        manual_beam_find=None,
        event_filter=None,
+        polarised=False,


Is it really necessary to have a polarised keyword?

andyfaff · 2020-12-02T01:47:22Z

refnx/reduce/reduce.py

+
+    Parameters
+    ----------
+    pp : PlatypusNexus object


the docstring doesn't correspond to the parameters and how they're used later in the function

Also in wrong order.

andyfaff · 2020-12-02T04:23:05Z

refnx/reduce/reduce.py

+        raw11.processed_spectrum["m_spec_polcorr"] = np.asarray(
+            [[val[0] for val in I11]]
+        )
+    elif pm is None and mp is not None:


is it necessary to duplicate this section?

andyfaff · 2020-12-02T23:44:56Z

refnx/reduce/reduce.py

+
+    # Create efficiency matrices from individual
+    # component efficiency matrices
+    efficiencies_matrix = [


I think this can be vectorised. If flipper1_eff_matrix, flipper2_eff_matrix, polariser_eff_matrix, analyser_eff_matrix all have the same shape (wavelength.size, 4, 4) then I think one can just do:

flipper1_eff_matrix @ flipper2_eff_matrix @ polariser_eff_matrix @ analyser_eff_matrix

andyfaff · 2020-12-02T23:47:24Z

refnx/reduce/reduce.py

+    # Invert efficiency matrices for each wavelength
+    inv_eff_matrix = [
+        np.linalg.inv(eff_mat) for eff_mat in efficiencies_matrix
+    ]


inv_eff_matrix = np.array(list(map(np.linalg.inv, efficiencies_matrix)))?

refnx/reduce/reduce.py

andyfaff · 2020-12-02T23:52:29Z

refnx/reduce/reduce.py

+    data : PlatypusNexus object
+        Polarised spectra for a given spin channel
+    channel : tuple
+        nominal spin channel - (0,0), (0,1), (1,0), or (1,1)


not clear what (0, 0) is. Is this mm or uu?
Perhaps we should use enumerations here?

andyfaff · 2020-12-03T00:16:55Z

refnx/reduce/reduce.py

+                        PlatypusNexus or None,
+                        PlatypusNexus or None,
+                        PlatypusNexus or None
+    The corrected datasets within the PlatypusNexus


Mention what combinations are accepted.

++, --
++, --, +-
++, --, +-, -+

andyfaff · 2020-12-03T00:17:36Z

refnx/reduce/reduce.py

+
+    # Check if R++ or R-- channel is missing
+    if mm is None:
+        print("Error: Missing R-- channel")


raise RuntimeError("Missing R-- channel")

andyfaff · 2020-12-03T00:19:10Z

refnx/reduce/reduce.py

+
+
+def polarised_correction(
+    mm=None, mp=None, pm=None, pp=None, reduction_options=None


make pp and mm positional parameters, no keyword.

andyfaff · 2020-12-03T00:19:59Z

refnx/reduce/reduce.py

+        print("Error: Input for +- channel doesn't match flipper statuses!")
+        return -1
+    elif mm is not None and _check_spin_channel(mm, (0, 0)) is False:
+        print("Error: Input for -- channel doesn't match flipper statuses!")


Exceptions for all of these.

andyfaff · 2020-12-03T00:22:53Z

refnx/reduce/reduce.py

+
+    # Initialise reduction options if not passed to function
+    if reduction_options is None:
+        reduction_options = {


options = ReductionOptions(lo_wavelength=2.5, hi_wavelength=12.5) options.update(reduction_options)

andyfaff · 2020-12-03T00:34:46Z

refnx/reduce/reduce.py

+
+    Returns
+    -------
+    I00, I01, I10, I11 : PlatypusNexus object


you're not returning the PN objects, you're returning the spectra.

andyfaff · 2020-12-03T00:39:53Z

refnx/reduce/reduce.py

+        for f1l in F1
+    ]
+    # Define flipper 2 efficiency matrix
+    flipper2_eff_matrix = [


andyfaff · 2020-12-03T00:44:09Z

refnx/reduce/reduce.py

+    p1a = 0.993
+    p1b = 0.57
+    p1c = 0.47
+    P1 = p1a - p1b * p1c ** (wavelength).astype("float")


@np.vectorize def efficiency_matrix(wavelength, tuple_of_spin_channels): # return 4*4 array

andyfaff · 2020-12-03T00:50:15Z

refnx/reduce/reduce.py

+        )
+    ]
+
+    I00_polcorr = [corr_pt[0] for corr_pt in np.array(corrected_data)]


we should be returning an array

andyfaff · 2020-12-03T00:54:04Z

refnx/reduce/reduce.py

+
+    for channel in _not_none(mm, mp, pm, pp):
+        if not channel.processed_spectrum:
+            channel.process(**reduction_options)


(**options)

andyfaff · 2020-12-03T00:55:14Z

refnx/reduce/reduce.py

+            I10=raw10.processed_spectrum["m_spec"][0],
+            I11=raw11.processed_spectrum["m_spec"][0],
+        )
+        raw00.processed_spectrum["m_spec_polcorr"] = np.asarray(


don't convert to arrays here, do it in correct_POL_efficiencies

andyfaff · 2020-12-03T00:55:48Z

refnx/reduce/reduce.py

+        )
+        raw01 = None
+        raw10 = None
+        raw11.processed_spectrum["m_spec_polcorr"] = np.asarray(


do array in correct_POL_efficiences

andyfaff · 2020-12-03T00:59:11Z

refnx/reduce/reduce.py

+
+    Returns
+    -------
+    I00, I01, I10, I11 : PlatypusNexus or None,


NSF aren't going to be None

Added SpinChannel Enum class that gets assigned to the spin_state attribute of PlatypusNexus objects based of the flipper1 and flipper2 statuses.

Uses Enum spin state class to arrange the scan's spin states to 00, 01, 10, 11. Change workings in polarised_correction to use I00, I01, I10, I11 for raw flipper statuses and mm, mp, pm, pp for corrected spin channels

PolarisedReduce encompasses all data for a typical reduction of polarised neutron reflectometry data. It needs direct beams for initialisation, that is made into a SpinSet which creates a PlatypusReduce object for each spin channel measured. TODO: add reflected beams into object for reduction SpinSet is an class to keep a spin set for a given angle together. it creates a PLatypusReduce object for each spin channel. TODO: incorporate polarisation correction in the initialisation routine Added both classes to __init__.py

More work on SpinSet so it works as expected now, and moved to platypusnexus.py file as I think it fits here more.

…to PNR_correction

…ection

…asses

andyfaff · 2021-03-30T05:33:16Z

@ohcpaull please have a look at andyfaff#9 for what I think PNR reduction should look like.

andyfaff · 2021-03-30T05:33:38Z

We should talk on Thursday.

ohcpaull and others added 19 commits October 28, 2020 16:33

STY: Fix styling for flake8

a9fcfe4

ADD: reduce tests and fix bits and pieces

3fd5519

Include a processing step in polarised_correction, and added some comments

FIX: Update efficiency correction from np.matrix to np.array

915dc9b

np.matrix will be deprecated eventually.

FIX: Sort out checks for variable number of spin channel inputs

6e7bd96

FIX: Fix __init__ imports

4356319

FIX: test_reduce.py file loading

fc42501

STY: Fix styling for black and flake8

b9c47fb

STY: Fix styling for flake8

a53b182

ADD: reduce tests and fix bits and pieces

c7cc57d

Include a processing step in polarised_correction, and added some comments

FIX: Update efficiency correction from np.matrix to np.array

d8d7c7b

np.matrix will be deprecated eventually.

FIX: Sort out checks for variable number of spin channel inputs

3aca20b

FIX: Fix __init__ imports

659a46d

FIX: test_reduce.py file loading

5dfe80b

STY: Fix styling for black and flake8

0fa622a

PEP8 + black

d2d531b

andyfaff force-pushed the PNR_correction branch from b9c47fb to d2d531b Compare December 2, 2020 00:56

MAINT: minor cleanups

03d675f

andyfaff reviewed Dec 2, 2020

View reviewed changes

andyfaff reviewed Dec 3, 2020

View reviewed changes

refnx/reduce/reduce.py

for f1l in F1

]

# Define flipper 2 efficiency matrix

flipper2_eff_matrix = [

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np.array([

andyfaff reviewed Dec 3, 2020

View reviewed changes

refnx/reduce/reduce.py

)

]

I00_polcorr = [corr_pt[0] for corr_pt in np.array(corrected_data)]

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we should be returning an array

andyfaff reviewed Dec 3, 2020

View reviewed changes

refnx/reduce/reduce.py Outdated

Returns

-------

I00, I01, I10, I11 : PlatypusNexus or None,

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NSF aren't going to be None

ohcpaull and others added 11 commits January 12, 2021 11:21

ADD: Enum-type class to store spin state

5494e94

Added SpinChannel Enum class that gets assigned to the spin_state attribute of PlatypusNexus objects based of the flipper1 and flipper2 statuses.

ADD: arrange_spin_channels

9a9f618

Uses Enum spin state class to arrange the scan's spin states to 00, 01, 10, 11. Change workings in polarised_correction to use I00, I01, I10, I11 for raw flipper statuses and mm, mp, pm, pp for corrected spin channels

MAINT: SpinSet and PolarisedReduce

d04601a

More work on SpinSet so it works as expected now, and moved to platypusnexus.py file as I think it fits here more.

Merge branch 'PNR_correction' of https://github.com/ohcpaull/refnx in…

4c9e6ad

…to PNR_correction

Merge branch 'master' of https://github.com/refnx/refnx into PNR_corr…

c797bd5

…ection

DEL: Get rid of PolarisedReduce class in this branch. Moved to PNR_cl…

8af107f

…asses

Touching up new classes

e6ed816

include polarised_correction in __init__

33578d7

FIX: Updated SpinSet class to newest version

b08c342

FIX: include underscore for SpinChannel checks

3bec13f

andyfaff closed this May 25, 2021

ohcpaull deleted the PNR_correction branch July 28, 2021 10:33



		def polarised_correction(
		mm=None, mp=None, pm=None, pp=None, reduction_options=None

Polarisation efficiency correction #510

Polarisation efficiency correction #510

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ohcpaull commented Nov 1, 2020

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andyfaff commented Mar 30, 2021

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