PyEBSDIndex 0.3.9 release

.github/workflows/publish.yml

@@ -29,10 +29,10 @@ jobs:
       # IMPORTANT: this permission is mandatory for trusted publishing:
       id-token: write
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
 
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.x'
 

.github/workflows/tests.yml

@@ -20,9 +20,9 @@ jobs:
     name: check manifest
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: '3.11'
 
@@ -49,10 +49,10 @@ jobs:
             DEPENDENCIES: matplotlib==3.3 numba==0.55.1 ray[default]==2.9
             LABEL: -oldest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
 

CHANGELOG.rst

@@ -5,30 +5,68 @@ Changelog
 All notable changes to PyEBSDIndex will be documented in this file. The format is based
 on `Keep a Changelog <https://keepachangelog.com/en/1.1.0>`_.
 
+
+0.3.9 (2026-01-26)
+==================
+
+Added
+-----
+- Now have the ability to save an indexer object to an HDF5 file using
+  the ``ebsd_index.indexer.saveindexer(filename='indexer.pyindx')`` method.  It can similarly be
+  restored using the ``indexer_obj = ebsd_index.restoreindexer(filename='indexer.pyindx')`` function.
+  This should be considered a beta-level capability, as there might be situations that yield incompatible
+  values for HDF5 and variable that are defined as ``None``.
+
+- Some preliminary support for DM5 files for use in the NLPAR algorithm.
+
+Changed
+-------
+- The band indexing steps in the ``triplevote`` module are now mostly multi-threaded using Numba.
+  This causes a long delay on the first index process, but should be much faster overall, espeically when
+  indexing using a single process mode (non-distributed).
+
+- Rebalanced the default number of processes used when using the distributed (aka multi-process) indexing,
+  given that the band indexing is now multi-threaded.
+
+- NLPAR now always breaks a scan into blocks of patterns, rather than defaulting to always using a full
+  row of patterns.  This was always the case for the GPU version of NLPAR, but now also works for the CPU version,
+  and hopefully prevents memory issues for larger scans on machines with lower RAM totals.
+
+- the ``EBSDImage.IPFcolor`` and ``EBSDImage.scalarimage`` now use the keywords ``ncols`` and ``nrows`` to
+  keep some consistency with the rest of the package.  ``xsize`` and ``ysize`` will still be respected for backwards
+  compatibility, but at some point in the future will be depreciated.
+
+
+Fixed
+-----
+- openCL should now stop spewing warning messages about reuse of programming objects.
+
+
+
 0.3.8 (2025-04-01)
 ==================
 
 Added
 -----
 - Ability to add micron bars to IPF and scalar values maps. Use the ``addmicronbar`` keyword
-to ``makeipf`` and ``scalarimage`` functions.
+  to ``makeipf`` and ``scalarimage`` functions.
 - When using ``ebsd_index`` function, if the machine has multiple GPUs, the desired GPU
-can be chosen using the ``gpu_id`` keyword.
+  can be chosen using the ``gpu_id`` keyword.
 - When making IPF maps, a grayscale mix can be added using ``graychannel`` keyword.
 - New pattern quality parameter, ``iq`` which is the mean intensity of the convolved peaks
-divided by the mean intensity of the radon.  Typical values are 1.8--2.0
+  divided by the mean intensity of the radon.  Typical values are 1.8--2.0
 - Initial support for Thermo-Fisher ``.pat`` files.
 
 Changed
 -------
 - Minimum official support is now python 3.9
 - pyebsdinex[parallel] now uses a minimum Ray v2.9
 - oh5 files are currently written with OIM 8.6.
-OIM 9.1 oh5 files can be specified using ``version=9.1``
+  OIM 9.1 oh5 files can be specified using ``version=9.1``
 - The ``fit`` value now is the _unweighted_ mean angular deviation. Previously this was
-the weighted eigen value from the QUEST algorithm.
+  the weighted eigen value from the QUEST algorithm.
 - Automatic CPU scheduling is changed for distributed indexing, avoiding spinning up many
-processes on large workstations.
+  processes on large workstations.
 
 
 Fixed

doc/tutorials/NLPAR_demo.ipynb

@@ -10,17 +10,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "id": "257eb666-089b-45c8-9350-70d5bbd1c2ed",
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pyebsdindex import nlpar"
+    "from pyebsdindex import nlpar\n",
+    "#from pyebsdindex import nlpar_cpu as nlpar"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "id": "307a4120-d677-4a3b-a496-9d247839c852",
    "metadata": {},
    "outputs": [],
@@ -30,7 +31,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "id": "8207251c-fd5a-41ae-a43e-ef8e4f05fb49",
    "metadata": {},
    "outputs": [],
@@ -66,35 +67,35 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "id": "83a724b4-120f-408b-834e-f05e17cda4b4",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Chunk size set to nrows: 278\n",
-      "Block 0\n"
+      "The number of scan columns is set to one, which is unusual, and may indicate that\n",
+      "the number of columns is not saved as metadata in the pattern file. Consider manually\n",
+      "entering the number of columns/rows with ``nlobj.ncols={number of your scan columns}`` and \n",
+      "``nlobj.nrows={number of your scan rows}``.\n",
+      "The number of scan columns is set to one, which is unusual, and may indicate that\n",
+      "the number of columns is not saved as metadata in the pattern file. Consider manually\n",
+      "entering the number of columns/rows with ``nlobj.ncols={number of your scan columns}`` and \n",
+      "``nlobj.nrows={number of your scan rows}``.\n",
+      "Range of lambda values:  [0.001      0.001      0.41923828]\n",
+      "Optimal Choice:  0.001\n"
      ]
     },
     {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "OMP: Info #276: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Block 278\n",
-      "Block 556\n",
-      "Block 834\n",
-      "Range of lambda values:  [0.65239258 0.90292969 1.15952148]\n",
-      "Optimal Choice:  0.9029296874999998\n"
-     ]
+     "data": {
+      "text/plain": [
+       "array([0.001     , 0.001     , 0.41923828])"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
     }
    ],
    "source": [
@@ -125,13 +126,19 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Chunk size set to nrows: 278\n",
-      "0.90292966 4 0.0\n",
-      "Block 0\n",
-      "Block 278\n",
-      "Block 556\n",
-      "Block 834\n"
+      "lambda: 0.9039062 search radius: 4 dthresh: 0.0\n",
+      "tiles complete: 36/36\r"
      ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "'/Users/dave/Desktop/SLMtest/scan2v3_NLPAR_l0.90sr4.up1'"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
     }
    ],
    "source": [
@@ -199,7 +206,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3.9.13 ('PyEBSDIndex')",
+   "display_name": "PyEBSDIndex",
    "language": "python",
    "name": "python3"
   },
@@ -213,12 +220,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
-  },
-  "vscode": {
-   "interpreter": {
-    "hash": "3cacad8e052162ebde31eae56cfe36e34759a2ea87d5d6503dd4028aeda06101"
-   }
+   "version": "3.11.11"
   }
  },
  "nbformat": 4,

pyebsdindex/EBSDImage/IPFcolor.py

@@ -37,8 +37,17 @@
 from pyebsdindex.EBSDImage import micronbar, scalarimage
 
 
-def makeipf(ebsddata, indexer, vector=np.array([0,0,1.0]), xsize = None, ysize = None,
-            addmicronbar=False, graychannel=None, gamma=1.0, **kwargs):
+def makeipf(ebsddata, indexer, vector=np.array([0,0,1.0]), ncols = None, nrows = None,
+            addmicronbar=False, graychannel=None, gamma=1.0,
+            xsize = None, ysize = None,  # these are kept for backwards compatability.
+            **kwargs):
+
+  # kept around for backwards compatability.
+  if xsize is not None:
+    ncols=xsize
+  if ysize is not None:
+    nrows = ysize
+
   nphase = len(indexer.phaseLib)
 
   npoints = ebsddata.shape[-1]
@@ -57,42 +66,39 @@ def makeipf(ebsddata, indexer, vector=np.array([0,0,1.0]), xsize = None, ysize =
   ipfout[ebsddata[-1]['fit'] > 179,:] = 0
 
 
-  if xsize is not None:
-    xsize = int(xsize)
-    #if ysize is None:
-      #print(ysize)
+  if ncols is not None:
+    ncols = int(ncols)
+
   else:
-    xsize = indexer.fID.nCols
-    #xsize = int(npoints)
-    #ysize = 1
+    ncols = indexer.fID.nCols
 
-  if ysize is not None:
-    ysize = int(ysize)
+
+  if nrows is not None:
+    nrows = int(nrows)
   else:
-    ysize = int(npoints // xsize + np.int64((npoints % xsize) > 0))
+    nrows = int(npoints // ncols + np.int64((npoints % ncols) > 0))
 
 
-  ipf_out = np.zeros((ysize, xsize,3), dtype=np.float32)
+  ipf_out = np.zeros((nrows, ncols, 3), dtype=np.float32)
   ipf_out = ipf_out.flatten()
-  npts = min(int(npoints), int(xsize*ysize))
-  # if int(xsize*ysize) < npoints:
-  #   npts = int(xsize*ysize)
+  npts = min(int(npoints), int(ncols * nrows))
+
   ipf_out[0:npts*3] = ipfout[0:npts,:].flatten()
-  ipf_out = ipf_out.reshape(ysize, xsize, 3)
+  ipf_out = ipf_out.reshape(nrows, ncols, 3)
 
   if graychannel is not None:
     if graychannel == 'fit':
       gchan = 'fitinv'
     else:
       gchan = graychannel
     gray = scalarimage.scalarimage(ebsddata, indexer,
-                       xsize=xsize,
-                       ysize=ysize,
-                       addmicronbar=False,
-                       datafield=gchan,
-                       cmap='gray',
-                       rescalenice=True, **kwargs
-                       )
+                                   ncols=ncols,
+                                   nrows=nrows,
+                                   addmicronbar=False,
+                                   datafield=gchan,
+                                   cmap='gray',
+                                   rescalenice=True, **kwargs
+                                   )
     ipf_out *= gray**gamma