fixes from pull request review

hexrd/cli/find_orientations.py

@@ -1,11 +1,16 @@
 from __future__ import print_function, division, absolute_import
 
 import os
+import logging
+import sys
+
 import numpy as np
 
 from hexrd import constants as const
+from hexrd import config
 from hexrd import instrument
 from hexrd.transforms import xfcapi
+from hexrd.findorientations import find_orientations, write_scored_orientations
 
 
 descr = 'Process rotation image series to find grain orientations'
@@ -52,10 +57,7 @@ def configure_parser(sub_parsers):
 
 def write_results(results, cfg):
     # Write scored orientations.
-    np.savez_compressed(
-        cfg.find_orientations.orientation_maps.scored_orientations_file,
-        **results['scored_orientations']
-    )
+    write_scored_orientations(results, cfg)
 
     # Write accepted orientations.
     qbar_filename = str(cfg.find_orientations.accepted_orientations_file)
@@ -73,12 +75,6 @@ def write_results(results, cfg):
 
 
 def execute(args, parser):
-    import logging
-    import sys
-
-    from hexrd import config
-    from hexrd.findorientations import find_orientations
-
     # make sure hkls are passed in as a list of ints
     try:
         if args.hkls is not None:

hexrd/cli/fit_grains.py

@@ -183,7 +183,6 @@ def execute(args, parser):
                 raise(RuntimeError,
                       "error loading indexing results '%s'" % quats_f)
         else:
-            quats_f = cfg.find_orientations.accepted_orientations_file
             logger.info("Missing %s, running find-orientations", quats_f)
             logger.removeHandler(ch)
             results = find_orientations(cfg)

hexrd/config/fitgrains.py

@@ -34,8 +34,6 @@ def tth(self):
 
 class FitGrainsConfig(Config):
 
-    _fit_grains = "fit-grains"
-
     def _active_material_str(self):
         return self.parent.material.active.strip().replace(' ', '-')
 
@@ -47,7 +45,7 @@ def __init__(self, cfg):
     @property
     def logfile(self):
         """Name of log file"""
-        return self.parent.analysis_dir / f"fit-grains.log"
+        return self.parent.analysis_dir / "fit-grains.log"
 
     @property
     def grains_file(self):

hexrd/config/root.py

@@ -21,22 +21,23 @@ class RootConfig(Config):
     def working_dir(self):
         """Working directory, either specified in file or current directory
 
-        This directory is certain to exist. If the specified directory does
-        not exist, it defaults to the current working directory.
+        If the directory is not specified in the config file, then it will
+        default to the current working directory. If it is specified, the
+        director must exist, or it will throw and IOError.
         """
-        try:
-            temp = Path(self.get('working_dir'))
-            if not temp.exists():
-                raise IOError(f'"working_dir": {temp} does not exist')
-            return temp
-
-        except RuntimeError:
-            temp = Path.cwd()
-            self.working_dir = temp
+        wdir = self.get('working_dir', default=None)
+        if wdir is not None:
+            wdir = Path(wdir)
+            if not wdir.exists():
+                raise IOError(f'"working_dir": {str(wdir)} does not exist')
+        else:
+            # Working directory has not been specified, so we use current
+            # directory.
+            wdir = Path.cwd()
             logger.info(
-                '"working_dir" not specified, defaulting to "%s"' % temp
-                )
-            return temp
+                '"working_dir" not specified, defaulting to "%s"' % wdir
+            )
+        return wdir
 
     @working_dir.setter
     def working_dir(self, val):
@@ -47,7 +48,7 @@ def working_dir(self, val):
 
     @property
     def analysis_name(self):
-        """Name (Path) of the analysis
+        """Name of the analysis
 
         This will be used to set up the output directory. The name can
         contain slash ("/") characters, which will generate a subdirectory
@@ -64,7 +65,7 @@ def analysis_dir(self):
         """Analysis directory, where output files go
 
         The name is derived from `working_dir` and `analysis_name`. This
-        propetry returns a Path object. The directory and any intermediate
+        property returns a Path object. The directory and any intermediate
         directories can be created with the `mkdir()` method, e.g.
 
         >>> analysis_dir.mkdir(parents=True, exist_ok=True)

hexrd/findorientations.py

@@ -42,6 +42,22 @@
 # =============================================================================
 
 
+def write_scored_orientations(results, fname):
+    """Write scored orientations to a file
+
+    PARAMETERS
+    ----------
+    results: dict
+       output of main `find_orientations` function
+    cfg: Config instance
+       the main Config input file for `find-orientations`
+    """
+    np.savez_compressed(
+        cfg.find_orientations.orientation_maps.scored_orientations_file,
+        **results['scored_orientations']
+    )
+
+
 def _process_omegas(omegaimageseries_dict):
     """Extract omega period and ranges from an OmegaImageseries dictionary."""
     oims = next(iter(omegaimageseries_dict.values()))
@@ -384,7 +400,10 @@ def quat_distance(x, y):
 
 def load_eta_ome_maps(cfg, pd, image_series, hkls=None, clean=False):
     """
-    Load the eta-ome maps specified by the config and CLI flags.
+    Load the eta-ome maps specified by the config and CLI flags. If the
+    maps file exists, it will return those values. If the file does not exist,
+    it will generate them using the passed HKLs (if not None) or the HKLs
+    specified in the config file (if passed HKLs are Noe).
 
     Parameters
     ----------
@@ -395,7 +414,7 @@ def load_eta_ome_maps(cfg, pd, image_series, hkls=None, clean=False):
     image_series: ImageSeries instance
         stack of images
     hkls: list, default = None
-        list of HKLs used in the eta-omega maps.
+        list of HKLs used to generate the eta-omega maps
     clean: bool, default = False
         flag indicating whether (if True) to overwrite existing maps file
 
@@ -415,7 +434,7 @@ def load_eta_ome_maps(cfg, pd, image_series, hkls=None, clean=False):
         try:
             res = EtaOmeMaps(str(fn))
             pd = res.planeData
-            logger.info(f'loaded eta/ome orientation maps from {str(fn)}')
+            logger.info(f'loaded eta/ome orientation maps from {fn}')
             shkls = pd.getHKLs(*res.iHKLList, asStr=True)
             logger.info(
                 'hkls used to generate orientation maps: %s',
@@ -429,7 +448,7 @@ def load_eta_ome_maps(cfg, pd, image_series, hkls=None, clean=False):
             )
             res = generate_eta_ome_maps(cfg, hkls=hkls)
 
-            filter_maps_if_requested(res, cfg)
+        filter_maps_if_requested(res, cfg)
     return res