Move project file into subpackage

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.dataobjects import HidraConstants
+from pyrs.projectfile import HidraProjectFile, HidraProjectFileMode
 from pyrs.utilities import checkdatatypes
-from pyrs.utilities.rs_project_file import HidraConstants, HidraProjectFile, HidraProjectFileMode
-import bisect
 
 
 class NeXusConvertingApp(object):

pyrs/core/powder_pattern.py

@@ -1,8 +1,8 @@
 from pyrs.core import reduction_manager
 from pyrs.utilities import checkdatatypes
 from pyrs.core import mask_util
+from pyrs.projectfile import HidraProjectFile, HidraProjectFileMode
 from pyrs.utilities import calibration_file_io
-from pyrs.utilities.rs_project_file import HidraProjectFile, HidraProjectFileMode
 from matplotlib import pyplot as plt
 
 

pyrs/core/pyrscore.py

@@ -1,9 +1,10 @@
 # This is the core of PyRS serving as the controller of PyRS and hub for all the data
 from pyrs.utilities import checkdatatypes
 from pyrs.core import instrument_geometry
+from pyrs.dataobjects import HidraConstants
 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 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.dataobjects import HidraConstants
+from pyrs.projectfile import HidraProjectFile, HidraProjectFileMode
+from pyrs.utilities import calibration_file_io
+from pyrs.utilities import checkdatatypes
 
 
 class HB2BReductionManager(object):

pyrs/core/workspaces.py

@@ -1,8 +1,8 @@
 # Data manager
 import numpy
-from pyrs.dataobjects import SampleLogs
+from pyrs.dataobjects import HidraConstants, SampleLogs
+from pyrs.projectfile import HidraProjectFile
 from pyrs.utilities import checkdatatypes
-from pyrs.utilities import rs_project_file
 
 
 class HidraWorkspace(object):
@@ -56,7 +56,7 @@ def _load_raw_counts(self, hidra_file):
         :param hidra_file:
         :return:
         """
-        checkdatatypes.check_type('HIDRA project file', hidra_file, rs_project_file.HidraProjectFile)
+        checkdatatypes.check_type('HIDRA project file', hidra_file, HidraProjectFile)
 
         for sub_run_i in self._sample_logs.subruns:
             counts_vec_i = hidra_file.read_raw_counts(sub_run_i)
@@ -71,7 +71,7 @@ def _load_reduced_diffraction_data(self, hidra_file):
         :return:
         """
         # Check inputs
-        checkdatatypes.check_type('HIDRA project file', hidra_file, rs_project_file.HidraProjectFile)
+        checkdatatypes.check_type('HIDRA project file', hidra_file, HidraProjectFile)
 
         # get 2theta value
         try:
@@ -123,7 +123,7 @@ def _load_instrument(self, hidra_file):
         :return:
         """
         # Check
-        checkdatatypes.check_type('HIDRA project file', hidra_file, rs_project_file.HidraProjectFile)
+        checkdatatypes.check_type('HIDRA project file', hidra_file, HidraProjectFile)
 
         # Get values
         self._instrument_setup = hidra_file.read_instrument_geometry()
@@ -135,7 +135,7 @@ def _load_sample_logs(self, hidra_file):
         :param hidra_file:  HIDRA project file instance
         :return:
         """
-        checkdatatypes.check_type('HIDRA project file', hidra_file, rs_project_file.HidraProjectFile)
+        checkdatatypes.check_type('HIDRA project file', hidra_file, HidraProjectFile)
 
         # overwrite the existing sample logs
         self._sample_logs = hidra_file.read_sample_logs()
@@ -145,7 +145,7 @@ def _load_wave_length(self, hidra_file):
         :param hidra_file:  HIDRA project file instance
         :return:
         """
-        checkdatatypes.check_type('HIDRA project file', hidra_file, rs_project_file.HidraProjectFile)
+        checkdatatypes.check_type('HIDRA project file', hidra_file, HidraProjectFile)
 
         # reset the wave length (dictionary) from HIDRA project file
         self._wave_length_dict = hidra_file.read_wavelengths()
@@ -158,11 +158,11 @@ 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 +173,14 @@ 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
@@ -257,7 +257,7 @@ def load_hidra_project(self, hidra_file, load_raw_counts, load_reduced_diffracti
         :return:
         """
         # Check input
-        checkdatatypes.check_type('HIDRA project file', hidra_file, rs_project_file.HidraProjectFile)
+        checkdatatypes.check_type('HIDRA project file', hidra_file, HidraProjectFile)
         self._project_file_name = hidra_file.name
 
         # create the spectrum map - must exist before loading the counts array
@@ -427,7 +427,7 @@ 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 +623,12 @@ 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
@@ -644,7 +644,7 @@ def save_reduced_diffraction_data(self, hidra_project):
         :param hidra_project: HidraProjectFile instance
         :return:
         """
-        checkdatatypes.check_type('HIDRA project file', hidra_project, rs_project_file.HidraProjectFile)
+        checkdatatypes.check_type('HIDRA project file', hidra_project, HidraProjectFile)
 
         hidra_project.write_reduced_diffraction_data_set(self._2theta_matrix, self._diff_data_set)
 

pyrs/dataobjects/__init__.py

@@ -0,0 +1,7 @@
+# flake8: noqa
+from __future__ import (absolute_import, division, print_function)  # python3 compatibility
+
+from .constants import *
+from .sample_logs import *
+
+__all__ = constants.__all__ + sample_logs.__all__

pyrs/dataobjects/constants.py

@@ -0,0 +1,43 @@
+__all__ = ['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'

pyrs/dataobjects.py → pyrs/dataobjects/sample_logs.py

@@ -1,6 +1,9 @@
 # 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.dataobjects import HidraConstants
+
+__all__ = ['SampleLogs']
 
 
 def _coerce_to_ndarray(value):
@@ -11,7 +14,7 @@ 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 +74,7 @@ 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/peaks/peak_fit_engine.py

@@ -1,7 +1,6 @@
 # This is the virtual base class as the fitting frame
 import numpy as np
 from pyrs.core import workspaces
-from pyrs.utilities import rs_project_file
 from pyrs.core import peak_profile_utility
 from pyrs.core.peak_profile_utility import PeakShape
 from pyrs.utilities import checkdatatypes
@@ -175,22 +174,23 @@ def estimate_peak_height(self, peak_range):
 
         return peak_heights, flat_bkgds
 
-    def export_to_hydra_project(self, hydra_project_file, peak_tag):
+    def export_to_hydra_project(self, hidra_project_file, peak_tag):
         """Export fit result from this fitting engine instance to Hidra project file
 
         Parameters
         ----------
-        hydra_project_file : pyrs.utilities.rs_project_file.HidraProjectFile
+        hidra_project_file : ~pyrs.projectfile.HidraProjectFile
         peak_tag
 
         Returns
         -------
 
         """
-        # Check input
-        checkdatatypes.check_type('Hidra project file', hydra_project_file, rs_project_file.HidraProjectFile)
-
-        hydra_project_file.write_peak_fit_result(self._peak_collection_dict[peak_tag])
+        try:
+            hidra_project_file.write_peak_fit_result(self._peak_collection_dict[peak_tag])
+        except AttributeError as e:
+            print 'Parameter "hidra_project_file" does not appear to be correct type', e
+            raise RuntimeError('Method requires a HidraProjectFile')
 
     def fit_peaks(self, peak_tag, sub_run_range, peak_function_name, background_function_name, peak_center,
                   peak_range, max_chi2=1E3, max_peak_shift=2, min_intensity=None):

pyrs/projectfile/__init__.py

@@ -0,0 +1,7 @@
+# flake8: noqa
+from __future__ import (absolute_import, division, print_function)  # python3 compatibility
+
+from .file_mode import *
+from .file_object import *
+
+__all__ = file_mode.__all__ + file_object.__all__

pyrs/projectfile/file_mode.py

@@ -0,0 +1,37 @@
+# This is rs_scan_io.DiffractionFile's 2.0 version
+from enum import Enum
+
+__all__ = ['HidraProjectFileMode']
+
+
+class HidraProjectFileMode(Enum):
+    '''
+    Enumeration for file access mode
+
+    These values match the strings of :py:obj:`h5py.File`
+    '''
+    READONLY = 'r'   # read-only
+    READWRITE = 'a'  # read and write
+    OVERWRITE = 'w'  # new file
+
+    def __str__(self):
+        return self.value
+
+    @staticmethod
+    def getMode(mode):
+        '''Private function to convert anything into :py:obj:`HidraProjectFileMode`'''
+        if mode in HidraProjectFileMode:
+            return mode  # already a member of the enum
+        else:
+            # all other checks are for strings
+            # the first checks are against nominal values
+            # the last check is against the enum names
+            mode = str(mode).lower()
+            if mode in ['a', 'rw']:
+                return HidraProjectFileMode.READWRITE
+            elif mode == 'r':
+                return HidraProjectFileMode.READONLY
+            elif mode == 'w':
+                return HidraProjectFileMode.OVERWRITE
+            else:
+                return HidraProjectFileMode[mode.upper()]