Moved HidraConstants into separate file refs #219

pyrs/core/nexus_conversion.py

@@ -2,15 +2,16 @@
 Convert HB2B NeXus file to Hidra project file for further reduction
 """
 from __future__ import (absolute_import, division, print_function)  # python3 compatibility
-from mantid.simpleapi import mtd, GenerateEventsFilter, LoadEventNexus, FilterEvents
+import bisect
 from mantid.kernel import FloatTimeSeriesProperty, Int32TimeSeriesProperty, Int64TimeSeriesProperty, logger, Logger
+from mantid.simpleapi import mtd, GenerateEventsFilter, LoadEventNexus, FilterEvents
 import numpy
 import os
 from pyrs.core import workspaces
 from pyrs.core.instrument_geometry import AnglerCameraDetectorGeometry, HidraSetup
+from pyrs.projectfile import HidraConstants
 from pyrs.utilities import checkdatatypes
-from pyrs.utilities.rs_project_file import HidraConstants, HidraProjectFile, HidraProjectFileMode
-import bisect
+from pyrs.utilities.rs_project_file import HidraProjectFile, HidraProjectFileMode
 
 
 class NeXusConvertingApp(object):

pyrs/core/pyrscore.py

@@ -3,7 +3,8 @@
 from pyrs.core import instrument_geometry
 from pyrs.utilities import file_util
 from pyrs.peaks import PeakFitEngineFactory, SupportedPeakProfiles, SupportedBackgroundTypes
-from pyrs.utilities.rs_project_file import HidraConstants, HidraProjectFile, HidraProjectFileMode
+from pyrs.projectfile import HidraConstants
+from pyrs.utilities.rs_project_file import HidraProjectFile, HidraProjectFileMode
 from pyrs.core import strain_stress_calculator
 from pyrs.core import reduction_manager
 from pyrs.core import polefigurecalculator
@@ -394,22 +395,16 @@ def load_hidra_project(self, hidra_h5_name, project_name, load_detector_counts=T
         Parameters
         ----------
         hidra_h5_name
+            name of HIDRA project file in HDF5 format
         project_name
+            name of the reduction project specified by user to trace
         load_detector_counts
         load_diffraction
 
         Returns
         -------
         pyrs.core.workspaces.HidraWorkspace
 
-        """
-        """
-        Load a HIDRA project file
-        :param hidra_h5_name: name of HIDRA project file in HDF5 format
-        :param project_name: name of the reduction project specified by user to trace
-        :param load_detector_counts:
-        :param load_diffraction:
-        :return: HidraWorkspace instance
         """
         # Initialize session
         self._reduction_service.init_session(project_name)

pyrs/core/reduction_manager.py

@@ -2,14 +2,15 @@
 import os
 import random
 import numpy as np
-from pyrs.utilities import checkdatatypes
 from pyrs.core import workspaces
-from pyrs.utilities import calibration_file_io
+from pyrs.core import instrument_geometry
 from pyrs.core import mask_util
 from pyrs.core import reduce_hb2b_mtd
 from pyrs.core import reduce_hb2b_pyrs
-from pyrs.utilities.rs_project_file import HidraProjectFile, HidraProjectFileMode, HidraConstants
-from pyrs.core import instrument_geometry
+from pyrs.projectfile import HidraConstants
+from pyrs.utilities import calibration_file_io
+from pyrs.utilities import checkdatatypes
+from pyrs.utilities.rs_project_file import HidraProjectFile, HidraProjectFileMode
 
 
 class HB2BReductionManager(object):

pyrs/core/workspaces.py

@@ -1,6 +1,7 @@
 # Data manager
 import numpy
 from pyrs.dataobjects import SampleLogs
+from pyrs.projectfile import HidraConstants
 from pyrs.utilities import checkdatatypes
 from pyrs.utilities import rs_project_file
 
@@ -158,11 +159,11 @@ def get_detector_2theta(self, sub_run):
         """
         checkdatatypes.check_int_variable('Sub run number', sub_run, (0, None))
         try:
-            two_theta = self._sample_logs[rs_project_file.HidraConstants.TWO_THETA, sub_run]
+            two_theta = self._sample_logs[HidraConstants.TWO_THETA, sub_run]
         except KeyError as key_err:
             raise RuntimeError('Unable to retrieve 2theta value ({}) from sub run {} due to missing key {}.'
                                'Available sample logs are {}'
-                               .format(rs_project_file.HidraConstants.TWO_THETA,
+                               .format(HidraConstants.TWO_THETA,
                                        sub_run, key_err, self._sample_logs.keys()))
         return two_theta[0]  # convert from numpy array of length 1 to a scalar
 
@@ -173,14 +174,14 @@ def get_l2(self, sub_run):
         """
         checkdatatypes.check_int_variable('Sub run number', sub_run, (0, None))
 
-        if rs_project_file.HidraConstants.L2 in self._sample_logs:
+        if HidraConstants.L2 in self._sample_logs:
             # L2 is a valid sample log: get L2
             try:
                 # convert from numpy array of length 1 to a scalar
-                l2 = self._sample_logs[rs_project_file.HidraConstants.L2, sub_run][0]
+                l2 = self._sample_logs[HidraConstants.L2, sub_run][0]
             except KeyError as key_err:
                 raise RuntimeError('Unable to retrieve L2 value for {} due to {}. Available sun runs are {}'
-                                   .format(sub_run, key_err, self._sample_logs[rs_project_file.HidraConstants.L2]))
+                                   .format(sub_run, key_err, self._sample_logs[HidraConstants.L2]))
         else:
             # L2 might be unchanged
             l2 = None
@@ -427,7 +428,7 @@ def get_sample_log_values(self, sample_log_name, sub_runs=None):
             sample log values ordered by sub run numbers with given sub runs or all sub runs
 
         """
-        if sample_log_name == rs_project_file.HidraConstants.SUB_RUNS and \
+        if sample_log_name == HidraConstants.SUB_RUNS and \
                 sample_log_name not in self._sample_logs.keys():
             return self.get_sub_runs()
 
@@ -623,12 +624,12 @@ def save_experimental_data(self, hidra_project, sub_runs=None):
         else:
             # same thing
             sub_runs_array = sub_runs
-        hidra_project.append_experiment_log(rs_project_file.HidraConstants.SUB_RUNS, sub_runs_array)
+        hidra_project.append_experiment_log(HidraConstants.SUB_RUNS, sub_runs_array)
 
         # Add regular ample logs
         for log_name in self._sample_logs.keys():
             # no operation on 'sub run': skip
-            if log_name == rs_project_file.HidraConstants.SUB_RUNS:
+            if log_name == HidraConstants.SUB_RUNS:
                 continue
 
             # Convert each sample log to a numpy array

pyrs/dataobjects.py

@@ -1,7 +1,7 @@
 # extentable version of dict https://treyhunner.com/2019/04/why-you-shouldnt-inherit-from-list-and-dict-in-python/
 from collections import MutableMapping
 import numpy as np
-
+from pyrs.projectfile import HidraConstants
 
 def _coerce_to_ndarray(value):
     if isinstance(value, np.ndarray):
@@ -11,7 +11,7 @@ def _coerce_to_ndarray(value):
 
 
 class SampleLogs(MutableMapping):
-    SUBRUN_KEY = 'sub-runs'  # TODO should be pyrs.utilities.rs_project_file.HidraConstants.SUB_RUNS
+    SUBRUN_KEY = HidraConstants.SUB_RUNS
 
     def __init__(self, **kwargs):
         self._data = dict(kwargs)
@@ -71,7 +71,7 @@ def __setitem__(self, key, value):
     def plottable_logs(self):
         '''Return the name of all logs that are plottable
 
-        This always includes :py:obj:`~pyrs.utilities.rs_project_file.HidraConstants.SUB_RUNS`
+        This always includes :py:obj:`~pyrs.projectfile.HidraConstants.SUB_RUNS`
         in addition to all the other logs'''
         return list(self._plottable)
 

pyrs/projectfile/__init__.py

@@ -0,0 +1,4 @@
+# flake8: noqa
+from .constants import HidraConstants
+
+__all__ = ['HidraConstants']

pyrs/projectfile/constants.py

@@ -0,0 +1,40 @@
+class HidraConstants(object):
+    """
+    Constants used for Hidra project file, workspace and related dictionary
+    """
+    RAW_DATA = 'raw data'
+    REDUCED_DATA = 'reduced diffraction data'
+    REDUCED_MAIN = 'main'   # default reduced data
+    SUB_RUNS = 'sub-runs'
+    CALIBRATION = 'calibration'
+    SAMPLE_LOGS = 'logs'
+    INSTRUMENT = 'instrument'
+    GEOMETRY_SETUP = 'geometry setup'
+    DETECTOR_PARAMS = 'detector'
+    TWO_THETA = '2theta'
+    L2 = 'L2'
+
+    MONO = 'monochromator setting'
+    WAVELENGTH = 'wave length'
+
+    # Efficiency
+    DETECTOR_EFF = 'efficiency calibration'
+    RUN = 'run number'
+
+    # Masks
+    MASK = 'mask'  # main entry name of mask
+    DETECTOR_MASK = 'detector'
+    SOLID_ANGLE_MASK = 'solid angle'
+
+    # constants about peak fitting
+    PEAK_PROFILE = 'peak profile'
+    PEAKS = 'peaks'  # main entry for fitted peaks' parameters
+    PEAK_FIT_CHI2 = 'chi2'
+    PEAK_PARAMS = 'parameters'  # peak parameter values
+    PEAK_PARAMS_ERROR = 'fitting error'  # peak parameters' fitting error
+    PEAK_PARAM_NAMES = 'parameter names'  # peak parameter names
+    PEAK_COM = 'C.O.M'  # peak's center of mass
+    BACKGROUND_TYPE = 'background type'
+
+    # Special sample logs
+    SUB_RUN_DURATION = 'sub-run duration'

pyrs/utilities/rs_project_file.py

@@ -8,48 +8,9 @@
 from pyrs.core.instrument_geometry import AnglerCameraDetectorGeometry, HidraSetup
 from pyrs.peaks import PeakCollection
 from pyrs.dataobjects import SampleLogs
+from pyrs.projectfile import HidraConstants
 
-
-class HidraConstants(object):
-    """
-    Constants used for Hidra project file, workspace and related dictionary
-    """
-    RAW_DATA = 'raw data'
-    REDUCED_DATA = 'reduced diffraction data'
-    REDUCED_MAIN = 'main'   # default reduced data
-    SUB_RUNS = 'sub-runs'
-    CALIBRATION = 'calibration'
-    SAMPLE_LOGS = 'logs'
-    INSTRUMENT = 'instrument'
-    GEOMETRY_SETUP = 'geometry setup'
-    DETECTOR_PARAMS = 'detector'
-    TWO_THETA = '2theta'
-    L2 = 'L2'
-
-    MONO = 'monochromator setting'
-    WAVELENGTH = 'wave length'
-
-    # Efficiency
-    DETECTOR_EFF = 'efficiency calibration'
-    RUN = 'run number'
-
-    # Masks
-    MASK = 'mask'  # main entry name of mask
-    DETECTOR_MASK = 'detector'
-    SOLID_ANGLE_MASK = 'solid angle'
-
-    # constants about peak fitting
-    PEAK_PROFILE = 'peak profile'
-    PEAKS = 'peaks'  # main entry for fitted peaks' parameters
-    PEAK_FIT_CHI2 = 'chi2'
-    PEAK_PARAMS = 'parameters'  # peak parameter values
-    PEAK_PARAMS_ERROR = 'fitting error'  # peak parameters' fitting error
-    PEAK_PARAM_NAMES = 'parameter names'  # peak parameter names
-    PEAK_COM = 'C.O.M'  # peak's center of mass
-    BACKGROUND_TYPE = 'background type'
-
-    # Special sample logs
-    SUB_RUN_DURATION = 'sub-run duration'
+__all__ = ['HidraProjectFileMode', 'DiffractionUnit', 'HidraProjectFile']
 
 
 class HidraProjectFileMode(Enum):

tests/data/convert_xray_data.py

@@ -7,7 +7,8 @@
 
 Note: most of the methods to parse HZB data are copied from script pyrscalibration.py
 """
-from pyrs.utilities.rs_project_file import HidraConstants, HidraProjectFile, HidraProjectFileMode
+from pyrs.projectfile import HidraConstants
+from pyrs.utilities.rs_project_file import HidraProjectFile, HidraProjectFileMode
 from pyrs.core.instrument_geometry import HidraSetup
 import numpy
 from skimage import io

tests/integration/test_autoreduction.py

@@ -1,7 +1,7 @@
 import os
 from pyrs.core.nexus_conversion import NeXusConvertingApp
 from pyrs.core.powder_pattern import ReductionApp
-from pyrs.utilities.rs_project_file import HidraConstants
+from pyrs.projectfile import HidraConstants
 from matplotlib import pyplot as plt
 import pytest
 

tests/integration/test_peak_fitting.py

@@ -97,7 +97,7 @@ def show_fit_result(self, show_effective_params):
                                                                effective_parameter=show_effective_params)
         # Plot peak width
         sub_run_vec = peak_params_matrix[:, 0]
-        peak_width = peak_params_matrix[:, 5]  # rs_project_file.HidraConstants.Peak_FWHM for pandas output
+        peak_width = peak_params_matrix[:, 5]  # pyrs.projectfile.HidraConstants.Peak_FWHM for pandas output
         plt.plot(sub_run_vec, peak_width, color='red', label='FWHM')
 
         # plt.show()

tests/unit/test_hidra_project_file.py

@@ -1,7 +1,8 @@
 """
 Test for reading and writing components to HiDRA project file
 """
-from pyrs.utilities.rs_project_file import HidraConstants, HidraProjectFile, HidraProjectFileMode
+from pyrs.projectfile import HidraConstants
+from pyrs.utilities.rs_project_file import HidraProjectFile, HidraProjectFileMode
 import os
 import numpy as np
 import datetime