From c544fefde6dafba46c53b64acccab543aa8ec8a2 Mon Sep 17 00:00:00 2001
From: Thomas Milburn <milburn.j.thomas@gmail.com>
Date: Thu, 12 Oct 2023 15:59:37 +0100
Subject: [PATCH] Updated docstrings which are missing choices (#507)

* Added more choices to comments

---------

Co-authored-by: Thomas Milburn <thomas.milburn@diamond.ac.uk>
---
 archive/cuda_extension/engines/DM_gpu.py | 1 +
 archive/cuda_extension/engines/DM_npy.py | 1 +
 archive/engines/DM.py                    | 1 +
 ptypy/core/data.py                       | 2 ++
 ptypy/core/illumination.py               | 1 +
 ptypy/core/manager.py                    | 4 ++++
 ptypy/core/ptycho.py                     | 4 ++++
 ptypy/core/sample.py                     | 1 +
 ptypy/engines/base.py                    | 1 +
 ptypy/engines/projectional.py            | 1 +
 10 files changed, 17 insertions(+)

diff --git a/archive/cuda_extension/engines/DM_gpu.py b/archive/cuda_extension/engines/DM_gpu.py
index 399eb143c..9e81ad7fa 100644
--- a/archive/cuda_extension/engines/DM_gpu.py
+++ b/archive/cuda_extension/engines/DM_gpu.py
@@ -57,6 +57,7 @@ class DMGpu(DMNpy):
     default = 'linear'
     type = str
     help = Subpixel interpolation; 'fourier','linear' or None for no interpolation
+    choices = ['fourier','linear',None]
 
     [update_object_first]
     default = True
diff --git a/archive/cuda_extension/engines/DM_npy.py b/archive/cuda_extension/engines/DM_npy.py
index f601a46dd..6fce4bc5d 100644
--- a/archive/cuda_extension/engines/DM_npy.py
+++ b/archive/cuda_extension/engines/DM_npy.py
@@ -55,6 +55,7 @@ class DMNpy(DM):
     default = 'linear'
     type = str
     help = Subpixel interpolation; 'fourier','linear' or None for no interpolation
+    choices = ['fourier','linear',None]
 
     [update_object_first]
     default = True
diff --git a/archive/engines/DM.py b/archive/engines/DM.py
index 50936bd42..1124158a2 100644
--- a/archive/engines/DM.py
+++ b/archive/engines/DM.py
@@ -55,6 +55,7 @@ class DM(PositionCorrectionEngine):
     default = 'linear'
     type = str
     help = Subpixel interpolation; 'fourier','linear' or None for no interpolation
+    choices = ['fourier','linear',None]
 
     [update_object_first]
     default = True
diff --git a/ptypy/core/data.py b/ptypy/core/data.py
index 636857bca..288def4bf 100644
--- a/ptypy/core/data.py
+++ b/ptypy/core/data.py
@@ -114,6 +114,7 @@ class PtyScan(object):
     default = data
     help = Determines what will be loaded in parallel
     doc = Choose from ``None``, ``'data'``, ``'common'``, ``'all'``
+    choices = ['data', 'common', 'all']
 
     [rebin]
     type = int
@@ -139,6 +140,7 @@ class PtyScan(object):
        <newline>
        Alternatively, a 3-tuple of booleans may be provided ``(do_transpose, 
        do_flipud, do_fliplr)``
+    choices = [0, 1, 2, 3, 4, 5, 6, 7]
     userlevel = 1
 
     [min_frames]
diff --git a/ptypy/core/illumination.py b/ptypy/core/illumination.py
index af5d4c06b..ddf1f98f7 100644
--- a/ptypy/core/illumination.py
+++ b/ptypy/core/illumination.py
@@ -130,6 +130,7 @@
     	 - *<template>* : one of the templates inillumination module
     	
     	In script, you may pass a numpy.ndarray here directly as the model. It is considered as incoming wavefront and will be propagated according to `propagation` with an optional `aperture` applied before.
+    choices = ['recon','stxm',None]
     userlevel = 0
 
     [photons]
diff --git a/ptypy/core/manager.py b/ptypy/core/manager.py
index 0d9d7d341..ec376c8ff 100644
--- a/ptypy/core/manager.py
+++ b/ptypy/core/manager.py
@@ -71,6 +71,7 @@ class ScanModel(object):
     default = farfield
     help = Propagation type
     doc = Either "farfield" or "nearfield"
+    choices = ['farfield', 'nearfield']
     userlevel = 1
 
     [ffttype]
@@ -78,6 +79,7 @@ class ScanModel(object):
     default = scipy
     help = FFT library
     doc = Choose from "numpy", "scipy" or "fftw"
+    choices = ['numpy', 'scipy', 'fftw']
     userlevel = 1
 
     [data]
@@ -906,6 +908,7 @@ class _Full(object):
        - ``'irregular'``: no assumption
       **[not implemented]**
     type = str
+    choices = ['achromatic', 'linear', 'irregular']
     userlevel = 2
 
     [coherence.probe_dispersion]
@@ -917,6 +920,7 @@ class _Full(object):
        - ``'irregular'``: no assumption
       **[not implemented]**
     type = str
+    choices = ['achromatic', 'linear', 'irregular']
     userlevel = 2
 
     [resolution]
diff --git a/ptypy/core/ptycho.py b/ptypy/core/ptycho.py
index 9686823a3..94bbef48a 100644
--- a/ptypy/core/ptycho.py
+++ b/ptypy/core/ptycho.py
@@ -82,6 +82,7 @@ class Ptycho(Base):
        - ``INSPECT``:  Object Information
        - ``DEBUG``:    Debug
     type = str, int
+    choices = ['CRITICAL', 'ERROR', 'WARNING', 'INFO', 'INSPECT', 'DEBUG']
     userlevel = 0
 
     [data_type]
@@ -90,6 +91,7 @@ class Ptycho(Base):
     doc = Reconstruction floating number precision (``'single'`` or
           ``'double'``)
     type = str
+    choices = ['single', 'double']
     userlevel = 1
 
     [run]
@@ -248,6 +250,7 @@ class Ptycho(Base):
     help = Options for default plotter or template name
     doc = Flexible layout for default plotter is not implemented yet. Please choose one of the
       templates ``'default'``,``'black_and_white'``,``'nearfield'``, ``'minimal'`` or ``'weak'``
+    choices = ['default', 'black_and_white', 'nearfield', 'minimal', 'weak']
     userlevel = 2
 
     [io.autoplot.dump]
@@ -269,6 +272,7 @@ class Ptycho(Base):
     help = Produce timings for benchmarking the performance of data loaders and engines
     doc = Switch to get timings and save results to a json file in p.io.home
         Choose ``'all'`` for timing data loading, engine_init, engine_prepare, engine_iterate and engine_finalize
+    choices = ['all', 'loading', 'engine_init', 'engine_prepare', 'engine_iterate', 'engine_finalize']
     userlevel = 2
 
     [scans]
diff --git a/ptypy/core/sample.py b/ptypy/core/sample.py
index bdb14b4f3..4998e65cb 100644
--- a/ptypy/core/sample.py
+++ b/ptypy/core/sample.py
@@ -36,6 +36,7 @@
       processed according to `process` in order to *simulate* a sample from e.g. a thickness
       profile.
     type = str, array
+    choices = ['recon', 'stxm', 'None']
     userlevel = 0
 
     [fill]
diff --git a/ptypy/engines/base.py b/ptypy/engines/base.py
index a7ffb6cee..67426c0ba 100644
--- a/ptypy/engines/base.py
+++ b/ptypy/engines/base.py
@@ -376,6 +376,7 @@ class PositionCorrectionEngine(BaseEngine):
     default = "fourier"
     type = str
     help = Error metric, can choose between "fourier" and "photon"
+    choices = ["fourier", "photon"]
     
     [position_refinement.record]
     default = False
diff --git a/ptypy/engines/projectional.py b/ptypy/engines/projectional.py
index ba72aa2db..440831ea4 100644
--- a/ptypy/engines/projectional.py
+++ b/ptypy/engines/projectional.py
@@ -39,6 +39,7 @@ class _ProjectionEngine(PositionCorrectionEngine):
     default = 'linear'
     type = str
     help = Subpixel interpolation; 'fourier','linear' or None for no interpolation
+    choices = ['fourier','linear',None]
 
     [update_object_first]
     default = True