Merge branch 'FABLE-3DXRD:master' into master

.readthedocs.yaml

@@ -0,0 +1,39 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+  jobs:
+    post_install:
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH python setup.py build_ext --inplace
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH python -m sphinx.ext.apidoc -o docs/sphx ImageD11
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/sphx/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#   - pdf
+#   - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+    - requirements: docs/sphx/requirements.txt

ImageD11/sinograms/dataset.py

@@ -139,15 +139,22 @@ def __init__(
         self._pk2d = None
         self._pk4d = None
 
+        self.dsfile = None
+
+        # paths for processed data
+        self.analysispath = None # default
+        # Loaded
         if filename is not None:
+            self.dsfile = filename
             self.load(filename)
-        # paths for processed data
-
-        self.analysispath = analysispath
+        # Supplied overwrites
+        if analysispath is not None: 
+            # Can be loaded with the dataset 
+            self.analysispath = analysispath
 
         self.update_paths()
 
-    def update_paths(self, force=False):
+    def update_paths(self, force=False, verbose = False):
         # paths for processed data
         # root of analysis for this dataset for this sample:
         self.analysispath_default = os.path.join(
@@ -161,7 +168,8 @@ def update_paths(self, force=False):
         )
         # at the moment, set self.dsfile to be the default
         # if save or load is ever called, this will be replaced
-        self.dsfile = self.dsfile_default
+        if self.dsfile is None:
+            self.dsfile = self.dsfile_default
         # They should be saved / loaded with the dataset.
         for name, extn in [
             ("pksfile", "_peaks_table.h5"),
@@ -181,6 +189,11 @@ def update_paths(self, force=False):
             if (getattr(self, name, None) is None) or force:
                 # Otherwise, these are the defaults.
                 setattr(self, name, os.path.join(self.analysispath, self.dsname + extn))
+                if verbose:
+                    print('updated', getattr( self, name, None ) )
+            else:
+                if verbose:
+                    print('not updated', getattr( self, name, None ) )
 
     def __repr__(self):
         r = []
@@ -802,6 +815,9 @@ def check_sparse(self):
 
     def save(self, h5name=None, h5group="/"):
         if h5name is None:
+            if os.path.exists( self.dsfile ):
+                h5name = self.dsfile
+
             # none supplied, so use default path
             h5name = self.dsfile_default
             # make sure parent directories exist
@@ -858,9 +874,15 @@ def save(self, h5name=None, h5group="/"):
         self.dsfile = h5name
 
     def load(self, h5name=None, h5group="/"):
+
         if h5name is None:
-            # none supplied, so use default path
-            h5name = self.dsfile_default
+            if os.path.exists( self.dsfile ):
+                h5name = self.dsfile
+            elif os.path.exists( self.dsfile_default ):
+                # none supplied, so use default path
+                h5name = self.dsfile_default
+            else:
+                raise Exception( "Filename for dataset not found")
 
         """ Recover this from a hdf5 file """
         with h5py.File(h5name, "r") as hin:

ImageD11/sym_u.py

@@ -203,6 +203,8 @@ def rhombohedralP():
     """ R3 primitive """
     return generate_group("z,x,y", "-z,-y,-x")
 
+trigonalP = rhombohedralP
+
 def tetragonal():
     """ P4 75"""
     return generate_group ( "-y,x,z", "-x,y,-z" )