Merge branch 'dev'

CHANGELOG.rst

@@ -8,6 +8,11 @@ This document records all notable changes to
 This project adheres to `PEP 440 -- Version Identification 
 and Dependency Specification <https://www.python.org/dev/peps/pep-0440/>`_.
 
+0.4.4 (22-10-13)
+-----------------
+- Bug fixes (x- and y-axis vectors failing to generate with imported HDF5 files)
+- Minor tweaks and improvements
+
 0.4.3 (22-08-03)
 ----------------
 - Spectrum and Hsi now moved to **data.spectra**. **This could break your fork if you have custom code.**

crikit/CRIkitUI.py

@@ -893,9 +893,8 @@ def fileOpenSuccess(self, success):
         if self.ui.actionUndo_Backup_Enabled.isChecked():
             try:
                 _BCPre.backup_pickle(self.hsi, self.bcpre.id_list[-1])
-            except Exception as e:
-                _traceback.print_exc(limit=1)
-                print(e)
+            except Exception:
+                _traceback.print_exc()
                 print('Error in pickle backup (Undo functionality)')
             else:
                 self.bcpre.backed_up()

crikit/__init__.py

@@ -14,4 +14,4 @@
 * Charles H. Camp Jr. <charles.camp@nist.gov>
 """
 
-__version__ = '0.4.3'
+__version__ = '0.4.4'

crikit/io/hdf5.py

@@ -21,7 +21,8 @@
 __all__ = ['hdf_import_data', 'hdf_import_data_macroraster']
 
 
-def hdf_import_data_macroraster(pth, filename, dset_list, output_cls_instance, config_dict=None):
+def hdf_import_data_macroraster(pth, filename, dset_list, output_cls_instance, config_dict=None, 
+                                interp_kind_spatial='linear', interp_kind_spectral='linear'):
     """
     Import dataset(s) from HDF file with each dset being a single line scan.
 
@@ -107,10 +108,11 @@ def hdf_import_data_macroraster(pth, filename, dset_list, output_cls_instance, c
             all_xs.extend(curr_x_vec.tolist())
             all_ys.extend([curr_y_pos])
 
-            intfcn = interp1d(curr_n_imgs_vec, curr_x_vec, kind='linear')
+            intfcn = interp1d(curr_n_imgs_vec, curr_x_vec, kind=interp_kind_spatial)
 
             int_fcn_intensity = interp1d(intfcn(np.arange(curr_slice.shape[0])),
-                                         curr_slice, axis=0, bounds_error=False, kind='linear', fill_value='extrapolate')
+                                         curr_slice, axis=0, bounds_error=False, kind=interp_kind_spectral,
+                                         fill_value='extrapolate')
 
             y_idx = find_nearest(y_vec, curr_y_pos)[1]
             output_cls_instance.data[y_idx, ...] = int_fcn_intensity(x_vec)
@@ -169,7 +171,6 @@ def hdf_import_data(pth, filename, dset_list, output_cls_instance=None):
                 output_cls_instance.data = np.zeros(dset_shp, dtype=dset_dtype_import)
                 fid[dset_list].read_direct(output_cls_instance.data)
 
-                # output_cls_instance.data = fid[dset_list].value
                 output_cls_instance.meta = lazy5.inspect.get_attrs_dset(fid, dset_list)
             elif isinstance(dset_list, list):
                 if len(dset_list) > 1:
@@ -198,9 +199,8 @@ def hdf_import_data(pth, filename, dset_list, output_cls_instance=None):
                     output_cls_instance.data = np.zeros(dset_shp, dtype=dset_dtype_import)
                     fid[dset_list].read_direct(output_cls_instance.data)
                 else:
-                    output_cls_instance.data = fid[dset_list].value.astype(dset_dtype_import)
+                    output_cls_instance.data = fid[dset_list][:].astype(dset_dtype_import)
 
-                # output_cls_instance.data = fid[dset_list].value
                 output_cls_instance.meta = lazy5.inspect.get_attrs_dset(fid, dset_list)
 
             elif isinstance(dset_list, list):
@@ -222,7 +222,6 @@ def hdf_import_data(pth, filename, dset_list, output_cls_instance=None):
                 output_cls_instance.data = np.zeros(dset_shp, dtype=dset_dtype_import)
                 fid[dset_list].read_direct(output_cls_instance.data)
 
-                # output_cls_instance.data = fid[dset_list].value
                 output_cls_instance.meta = lazy5.inspect.get_attrs_dset(fid, dset_list)
             elif isinstance(dset_list, list):
                 if len > 1:
@@ -249,7 +248,6 @@ def hdf_import_data(pth, filename, dset_list, output_cls_instance=None):
                 data = np.zeros(dset_shp, dtype=dset_dtype_import)
                 fid[dset_list].read_direct(data)
 
-                # data = fid[dset_list].value
                 meta = lazy5.inspect.get_attrs_dset(fid, dset_list)
             elif isinstance(dset_list, list):
                 for num, dname in enumerate(dset_list):

crikit/io/macros.py

@@ -15,9 +15,11 @@
 __all__ = ['import_hdf_nist_special', 'import_csv_nist_special1']
 
 
-def hdf_nist_special_macroraster(pth, filename, dset_list, output_cls_instance):
+def hdf_nist_special_macroraster(pth, filename, dset_list, output_cls_instance, 
+                                 interp_kind_spatial='linear', interp_kind_spectral='linear'):
     print('\n')
-    import_success = _hdf_import_data_macroraster(pth, filename, dset_list, output_cls_instance)
+    import_success = _hdf_import_data_macroraster(pth, filename, dset_list, output_cls_instance,
+                                                  interp_kind_spatial='linear', interp_kind_spectral='linear')
     if import_success is False:
         raise ValueError('hdf_import_data_macroraster failed')
         return False

crikit/io/meta_process.py

@@ -187,8 +187,16 @@ def meta_process(rosetta, output_cls_instance):
                 stop = output_cls_instance.shape[1]-1
                 units = 'pix'
 
+            if isinstance(start, _np.ndarray):
+                start = start[0]
+            if isinstance(stop, _np.ndarray):
+                stop = stop[0]
+            if isinstance(steps, _np.ndarray):
+                steps = steps[0]
+
             print('{} ({}): Start={}\tStop={}\tSteps={}'.format(label, units, start, stop, steps))
             # print('Start: {}, Stop: {}, Steps: {}'.format(start, stop, steps))
+
             output_cls_instance.x_rep.data = _np.squeeze(_np.linspace(start, stop, steps))
             output_cls_instance.x_rep.units = units
             output_cls_instance.x_rep.label = label
@@ -224,6 +232,13 @@ def meta_process(rosetta, output_cls_instance):
             if isinstance(label, bytes):
                 label = label.decode()
 
+            if isinstance(start, _np.ndarray):
+                start = start[0]
+            if isinstance(stop, _np.ndarray):
+                stop = stop[0]
+            if isinstance(steps, _np.ndarray):
+                steps = steps[0]
+
             if steps != output_cls_instance.shape[0]:
                 print('{} ({}): Start={}\tStop={}\tSteps={}'.format(label, units, start, stop, steps))
                 print('Warning: {}Steps assigned in meta data ({}) disagrees with datacube size ({})'.format(label, steps, output_cls_instance.shape[0]))

docs/build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 79acee3da732a2077d4e910c14203444
+config: 126e78dc37b63522d8e4d07dce0d2051
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/html/_modules/crikit/CRIkitUI.html

@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>crikit.CRIkitUI &#8212; CRIKit2 0.4.3 documentation</title>
+    <title>crikit.CRIkitUI &#8212; CRIKit2 0.4.4 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../../_static/nature.css" />
     <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js"></script>
@@ -24,7 +24,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../index.html">CRIKit2 0.4.3 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../index.html">CRIKit2 0.4.4 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">crikit.CRIkitUI</a></li> 
       </ul>
@@ -931,9 +931,8 @@ <h1>Source code for crikit.CRIkitUI</h1><div class="highlight"><pre>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">ui</span><span class="o">.</span><span class="n">actionUndo_Backup_Enabled</span><span class="o">.</span><span class="n">isChecked</span><span class="p">():</span>
             <span class="k">try</span><span class="p">:</span>
                 <span class="n">_BCPre</span><span class="o">.</span><span class="n">backup_pickle</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">hsi</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">bcpre</span><span class="o">.</span><span class="n">id_list</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
-            <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
-                <span class="n">_traceback</span><span class="o">.</span><span class="n">print_exc</span><span class="p">(</span><span class="n">limit</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
-                <span class="nb">print</span><span class="p">(</span><span class="n">e</span><span class="p">)</span>
+            <span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span>
+                <span class="n">_traceback</span><span class="o">.</span><span class="n">print_exc</span><span class="p">()</span>
                 <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Error in pickle backup (Undo functionality)&#39;</span><span class="p">)</span>
             <span class="k">else</span><span class="p">:</span>
                 <span class="bp">self</span><span class="o">.</span><span class="n">bcpre</span><span class="o">.</span><span class="n">backed_up</span><span class="p">()</span>
@@ -3908,7 +3907,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../index.html">CRIKit2 0.4.3 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../index.html">CRIKit2 0.4.4 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../index.html" >Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">crikit.CRIkitUI</a></li> 
       </ul>

docs/build/html/_modules/crikit/cri/algorithms/kk.html

@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>crikit.cri.algorithms.kk &#8212; CRIKit2 0.4.3 documentation</title>
+    <title>crikit.cri.algorithms.kk &#8212; CRIKit2 0.4.4 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../../../../_static/nature.css" />
     <script data-url_root="../../../../" id="documentation_options" src="../../../../_static/documentation_options.js"></script>
@@ -24,7 +24,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../../../index.html">CRIKit2 0.4.3 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../../index.html">CRIKit2 0.4.4 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">crikit.cri.algorithms.kk</a></li> 
       </ul>
@@ -274,7 +274,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../../../index.html">CRIKit2 0.4.3 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../../index.html">CRIKit2 0.4.4 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../../index.html" >Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">crikit.cri.algorithms.kk</a></li> 
       </ul>

docs/build/html/_modules/crikit/cri/error_correction.html

@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>crikit.cri.error_correction &#8212; CRIKit2 0.4.3 documentation</title>
+    <title>crikit.cri.error_correction &#8212; CRIKit2 0.4.4 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../../../_static/nature.css" />
     <script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
@@ -24,7 +24,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../../index.html">CRIKit2 0.4.3 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../index.html">CRIKit2 0.4.4 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">crikit.cri.error_correction</a></li> 
       </ul>
@@ -355,7 +355,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../../index.html">CRIKit2 0.4.3 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../index.html">CRIKit2 0.4.4 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">crikit.cri.error_correction</a></li> 
       </ul>

docs/build/html/_modules/crikit/cri/kk.html

@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>crikit.cri.kk &#8212; CRIKit2 0.4.3 documentation</title>
+    <title>crikit.cri.kk &#8212; CRIKit2 0.4.4 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../../../_static/nature.css" />
     <script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
@@ -24,7 +24,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../../index.html">CRIKit2 0.4.3 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../index.html">CRIKit2 0.4.4 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">crikit.cri.kk</a></li> 
       </ul>
@@ -363,7 +363,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../../index.html">CRIKit2 0.4.3 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../index.html">CRIKit2 0.4.4 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">crikit.cri.kk</a></li> 
       </ul>

docs/build/html/_modules/crikit/cri/merge_nrbs.html

@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>crikit.cri.merge_nrbs &#8212; CRIKit2 0.4.3 documentation</title>
+    <title>crikit.cri.merge_nrbs &#8212; CRIKit2 0.4.4 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../../../_static/nature.css" />
     <script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
@@ -24,7 +24,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../../index.html">CRIKit2 0.4.3 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../index.html">CRIKit2 0.4.4 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">crikit.cri.merge_nrbs</a></li> 
       </ul>
@@ -175,7 +175,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../../index.html">CRIKit2 0.4.3 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../index.html">CRIKit2 0.4.4 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">crikit.cri.merge_nrbs</a></li> 
       </ul>

docs/build/html/_modules/crikit/cri/tests/test_hilbert.html

@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>crikit.cri.tests.test_hilbert &#8212; CRIKit2 0.4.3 documentation</title>
+    <title>crikit.cri.tests.test_hilbert &#8212; CRIKit2 0.4.4 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../../../../_static/nature.css" />
     <script data-url_root="../../../../" id="documentation_options" src="../../../../_static/documentation_options.js"></script>
@@ -24,7 +24,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../../../index.html">CRIKit2 0.4.3 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../../index.html">CRIKit2 0.4.4 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">crikit.cri.tests.test_hilbert</a></li> 
       </ul>
@@ -116,7 +116,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../../../index.html">CRIKit2 0.4.3 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../../index.html">CRIKit2 0.4.4 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../../index.html" >Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">crikit.cri.tests.test_hilbert</a></li> 
       </ul>