ChessAnalysisPipeline 0.0.12__py3-none-any.whl → 0.0.13__py3-none-any.whl

CHAP/utils/general.py

@@ -1417,8 +1417,8 @@ def select_roi_2d(
 
 
 def select_image_indices(
-        a, axis, b=None, preselected_indices=None, min_range=None,
-        min_num_indices=2, max_num_indices=2, title=None,
+        a, axis, b=None, preselected_indices=None, axis_index_offset=0,
+        min_range=None, min_num_indices=2, max_num_indices=2, title=None,
         title_a=None, title_b=None, row_label='row index',
         column_label='column index', interactive=True):
     """Display a 2D image and have the user select a set of image
@@ -1435,7 +1435,10 @@ def select_image_indices(
     :type b: numpy.ndarray, optional
     :param preselected_indices: Preselected image indices,
         defaults to `None`.
-    :type preselected_roi: tuple(int), list(int), optional
+    :type preselected_indices: tuple(int), list(int), optional
+    :param axis_index_offset: Offset in axes index range and
+        preselected indices, defaults to `0`.
+    :type axis_index_offset: int, optional
     :param min_range: The minimal range spanned by the selected 
         indices, defaults to `None`
     :type min_range: int, optional
@@ -1531,12 +1534,14 @@ def select_image_indices(
             error_texts.pop()
         try:
             index = int(expression)
-            if not 0 <= index <= a.shape[axis]:
+            if (index < axis_index_offset
+                    or index >= axis_index_offset+a.shape[axis]):
                 raise ValueError
         except ValueError:
             change_error_text(
                 f'Invalid {row_column} index ({expression}), enter an integer '
-                f'between 0 and {a.shape[axis]-1}')
+                f'between {axis_index_offset} and '
+                f'{axis_index_offset+a.shape[axis]-1}')
         else:
             try:
                 add_index(index)
@@ -1585,9 +1590,13 @@ def select_image_indices(
         row_column = 'row'
     else:
         row_column = 'column'
+    if not is_int(axis_index_offset, ge=0, log=False):
+        raise ValueError(
+            'Invalid parameter axis_index_offset ({axis_index_offset})')
     if preselected_indices is not None:
         if not is_int_series(
-                preselected_indices, ge=0, le=a.shape[axis], log=False):
+                preselected_indices, ge=axis_index_offset,
+                le=axis_index_offset+a.shape[axis], log=False):
             if interactive:
                 logger.warning(
                     'Invalid parameter preselected_indices '
@@ -1607,7 +1616,7 @@ def select_image_indices(
         if a.shape[0] != b.shape[0]:
             raise ValueError(f'Inconsistent image shapes({a.shape} vs '
                              f'{b.shape})')
-        
+ 
     indices = []
     lines = []
     fig_title = []
@@ -1627,10 +1636,11 @@ def select_image_indices(
            fig, axs = plt.subplots(1, 2, figsize=(11, 8.5))
        else:
            fig, axs = plt.subplots(2, 1, figsize=(11, 8.5))
-    axs[0].imshow(a)
+    extent = (0, a.shape[1], axis_index_offset+a.shape[0], axis_index_offset)
+    axs[0].imshow(a, extent=extent)
     axs[0].set_title(title_a, fontsize='xx-large')
     if b is not None:
-        axs[1].imshow(b)
+        axs[1].imshow(b, extent=extent)
         axs[1].set_title(title_b, fontsize='xx-large')
         if a.shape[0]+b.shape[0] > max(a.shape[1], b.shape[1]):
             axs[0].set_xlabel(column_label, fontsize='x-large')
@@ -1641,8 +1651,8 @@ def select_image_indices(
             axs[1].set_xlabel(column_label, fontsize='x-large')
             axs[1].set_ylabel(row_label, fontsize='x-large')
     for ax in axs:
-        ax.set_xlim(0, a.shape[1])
-        ax.set_ylim(a.shape[0], 0)
+        ax.set_xlim(extent[0], extent[1])
+        ax.set_ylim(extent[2], extent[3])
     fig.subplots_adjust(bottom=0.0, top=0.85)
 
     # Setup the preselected indices if provided

CHAP/utils/scanparsers.py

@@ -49,7 +49,12 @@ class ScanParser:
 
         self._detector_data_path = None
 
-    def __repr__(self):
+        if isinstance(self, FMBRotationScanParser) and scan_number > 1:
+            scanparser = FMBRotationScanParser(spec_file_name, scan_number-1)
+            if (scanparser.spec_macro in ('rams4_step_ome', 'rams4_fly_ome')
+                    and len(scanparser.spec_args) == 5):
+                self._rams4_args = scanparser.spec_args
+
         return (f'{self.__class__.__name__}'
                 f'({self.spec_file_name}, {self.scan_number}) '
                 f'-- {self.spec_command}')
@@ -527,7 +532,17 @@ class FMBLinearScanParser(LinearScanParser, FMBScanParser):
 
     def get_spec_scan_motor_mnes(self):
         if self.spec_macro == 'flymesh':
-            return (self.spec_args[0], self.spec_args[5])
+            m1_mne = self.spec_args[0]
+            try:
+                # Try post-summer-2022 format
+                dwell = float(self.spec_args[4])
+            except:
+                # Accommodate pre-summer-2022 format
+                m2_mne_i = 4
+            else:
+                m2_mne_i = 5
+            m2_mne = self.spec_args[m2_mne_i]
+            return (m1_mne, m2_mne)
         if self.spec_macro in ('flyscan', 'ascan'):
             return (self.spec_args[0],)
         if self.spec_macro in ('tseries', 'loopscan'):
@@ -537,12 +552,26 @@ class FMBLinearScanParser(LinearScanParser, FMBScanParser):
 
     def get_spec_scan_motor_vals(self):
         if self.spec_macro == 'flymesh':
-            fast_mot_vals = np.linspace(float(self.spec_args[1]),
-                                        float(self.spec_args[2]),
-                                        int(self.spec_args[3])+1)
-            slow_mot_vals = np.linspace(float(self.spec_args[6]),
-                                        float(self.spec_args[7]),
-                                        int(self.spec_args[8])+1)
+            m1_start = float(self.spec_args[1])
+            m1_end = float(self.spec_args[2])
+            m1_npt = int(self.spec_args[3]) + 1
+            try:
+                # Try post-summer-2022 format
+                dwell = float(self.spec_args[4])
+            except:
+                # Accommodate pre-summer-2022 format
+                m2_start_i = 5
+                m2_end_i = 6
+                m2_nint_i = 7
+            else:
+                m2_start_i = 6
+                m2_end_i = 7
+                m2_nint_i = 8
+            m2_start = float(self.spec_args[m2_start_i])
+            m2_end = float(self.spec_args[m2_end_i])
+            m2_npt = int(self.spec_args[m2_nint_i]) + 1
+            fast_mot_vals = np.linspace(m1_start, m1_end, m1_npt)
+            slow_mot_vals = np.linspace(m2_start, m2_end, m2_npt)
             return (fast_mot_vals, slow_mot_vals)
         if self.spec_macro in ('flyscan', 'ascan'):
             mot_vals = np.linspace(float(self.spec_args[1]),
@@ -556,8 +585,16 @@ class FMBLinearScanParser(LinearScanParser, FMBScanParser):
 
     def get_spec_scan_shape(self):
         if self.spec_macro == 'flymesh':
-            fast_mot_npts = int(self.spec_args[3])+1
-            slow_mot_npts = int(self.spec_args[8])+1
+            fast_mot_npts = int(self.spec_args[3]) + 1
+            try:
+                # Try post-summer-2022 format
+                dwell = float(self.spec_args[4])
+            except:
+                # Accommodate pre-summer-2022 format
+                m2_nint_i = 7
+            else:
+                m2_nint_i = 8
+            slow_mot_npts = int(self.spec_args[m2_nint_i]) + 1
             return (fast_mot_npts, slow_mot_npts)
         if self.spec_macro in ('flyscan', 'ascan'):
             mot_npts = int(self.spec_args[3])+1
@@ -568,7 +605,15 @@ class FMBLinearScanParser(LinearScanParser, FMBScanParser):
                            f'for scans of type {self.spec_macro}')
 
     def get_spec_scan_dwell(self):
-        if self.spec_macro in ('flymesh', 'flyscan', 'ascan'):
+        if self.macro == 'flymesh':
+            try:
+                # Try post-summer-2022 format
+                dwell = float(self.spec_args[4])
+            except:
+                # Accommodate pre-summer-2022 format
+                dwell = float(self.spec_args[8])
+            return dwell
+        if self.spec_macro in ('flyscan', 'ascan'):
             return float(self.spec_args[4])
         if self.spec_macro in ('tseries', 'loopscan'):
             return float(self.spec_args[1])
@@ -609,8 +654,10 @@ class FMBSAXSWAXSScanParser(FMBLinearScanParser):
         return f'{self.scan_name}_{self.scan_number:03d}'
 
     def get_detector_data_file(self, detector_prefix, scan_step_index:int):
-        detector_files = list_fmb_saxswaxs_detector_files(self.detector_data_path, detector_prefix)
-        return os.path.join(self.detector_data_path, detector_files[scan_step_index])
+        detector_files = list_fmb_saxswaxs_detector_files(
+            self.detector_data_path, detector_prefix)
+        return os.path.join(
+            self.detector_data_path, detector_files[scan_step_index])
 
     def get_detector_data(self, detector_prefix, scan_step_index:int):
         image_file = self.get_detector_data_file(detector_prefix,
@@ -793,7 +840,17 @@ class FMBRotationScanParser(RotationScanParser, FMBScanParser):
     with the typical tomography setup at FMB.
     """
 
+    def get_spec_scan_data(self):
+        spec_scan_data = super().get_spec_scan_data()
+        if hasattr(self, '_rams4_args'):
+            spec_scan_data['theta'] = np.linspace(
+                float(self._rams4_args[0]), float(self._rams4_args[1]),
+                1+int(self._rams4_args[2]))
+        return spec_scan_data
+
     def get_spec_scan_npts(self):
+        if hasattr(self, '_rams4_args'):
+            return 1+int(self._rams4_args[2])
         if self.spec_macro == 'flyscan':
             if len(self.spec_args) == 2:
                 return 1+int(self.spec_args[0])
@@ -802,12 +859,12 @@ class FMBRotationScanParser(RotationScanParser, FMBScanParser):
             raise RuntimeError(f'{self.scan_title}: cannot obtain number of '
                                f'points from {self.spec_macro} with arguments '
                                f'{self.spec_args}')
-        elif self.spec_macro == 'ascan':
-            if len(self.spec_args) == 5:
-                return int(self.spec_args[3])
-            raise RuntimeError(f'{self.scan_title}: cannot obtain number of '
-                               f'points from {self.spec_macro} with arguments '
-                               f'{self.spec_args}')
+#        if self.spec_macro == 'ascan':
+#            if len(self.spec_args) == 5:
+#                return int(self.spec_args[3])
+#            raise RuntimeError(f'{self.scan_title}: cannot obtain number of '
+#                               f'points from {self.spec_macro} with arguments '
+#                               f'{self.spec_args}')
         raise RuntimeError(f'{self.scan_title}: cannot determine rotation '
                            f' angles for scans of type {self.spec_macro}')
 
@@ -815,21 +872,10 @@ class FMBRotationScanParser(RotationScanParser, FMBScanParser):
         return 0
 
     def get_starting_image_offset(self):
+        if hasattr(self, '_rams4_args'):
+            return int(self.spec_args[0]) - self.spec_scan_npts
         if self.spec_macro == 'flyscan':
-#            if len(self.spec_args) == 2:
-#                return 1
-#            if len(self.spec_args) == 5:
-#                return 1
             return 1
-#            raise RuntimeError(f'{self.scan_title}: cannot obtain starting '
-#                               f'image offset {self.spec_macro} with arguments'
-#                               f' {self.spec_args}')
-#        elif self.spec_macro == 'ascan':
-#            if len(self.spec_args) == 5:
-#                return 0
-#            raise RuntimeError(f'{self.scan_title}: cannot obtain starting '
-#                               f'image offset {self.spec_macro} with arguments'
-#                               f' {self.spec_args}')
         raise RuntimeError(f'{self.scan_title}: cannot determine starting '
                            f'image offset for scans of type {self.spec_macro}')
 
@@ -855,8 +901,6 @@ class FMBRotationScanParser(RotationScanParser, FMBScanParser):
             if scan_step_index is None:
                 detector_data = h5_file['/entry/instrument/detector/data'][
                     self.starting_image_offset:]
-#                sum_det = list(np.sum(detector_data, (1,2)))
-#                print(f'\n\nsum scanparser ({len(sum_det)}):\n{sum_det}')
             elif isinstance(scan_step_index, int):
                 detector_data = h5_file['/entry/instrument/detector/data'][
                     self.starting_image_offset+scan_step_index]
@@ -873,10 +917,8 @@ class FMBRotationScanParser(RotationScanParser, FMBScanParser):
     def get_detector_data(self, detector_prefix, scan_step_index=None):
         try:
             # Detector files in h5 format
-#            print('data in h5 file')
             detector_data = self.get_all_detector_data_in_file(
                 detector_prefix, scan_step_index)
-#            print(f'detector_data {detector_prefix} {scan_step_index}:\n{detector_data.shape}')
         except:
             # Detector files in tiff format
             if scan_step_index is None:
@@ -999,19 +1041,16 @@ class SMBRotationScanParser(RotationScanParser, SMBScanParser):
                            f'file for scan step ({scan_step_index})')
 
     def get_detector_data(self, detector_prefix, scan_step_index=None):
-#        print(f'\n\nin get_detector_data: {detector_prefix} {scan_step_index}')
         if scan_step_index is None:
             detector_data = []
             for index in range(self.spec_scan_npts):
                 detector_data.append(
                     self.get_detector_data(detector_prefix, index))
             detector_data = np.asarray(detector_data)
-#            print(f'detector_data shape {type(detector_data)} {detector_data.shape}:\n{detector_data}')
         elif isinstance(scan_step_index, int):
             image_file = self.get_detector_data_file(scan_step_index)
             with TiffFile(image_file) as tiff_file:
                 detector_data = tiff_file.asarray()
-#            print(f'\t{scan_step_index} {image_file} {np.sum(np.asarray(detector_data))}')
         elif (isinstance(scan_step_index, (list, tuple))
                 and len(scan_step_index) == 2):
             detector_data = []

{ChessAnalysisPipeline-0.0.12.dist-info → ChessAnalysisPipeline-0.0.13.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ChessAnalysisPipeline
-Version: 0.0.12
+Version: 0.0.13
 Summary: CHESS analysis pipeline framework
 Home-page: https://github.com/CHESSComputing/ChessAnalysisPipeline
 Author: Keara Soloway, Rolf Verberg, Valentin Kuznetsov

{ChessAnalysisPipeline-0.0.12.dist-info → ChessAnalysisPipeline-0.0.13.dist-info}/RECORD

@@ -1,15 +1,15 @@
 CHAP/TaskManager.py,sha256=NEqg2jAq10kbScE18XtzY3liqkIdAtysaR-gMG5tBzs,6803
-CHAP/__init__.py,sha256=CuEa7CS9G-sEmvUo4967SV7YF6tujP7UwkOgWoK7_ME,1052
+CHAP/__init__.py,sha256=fgkAhLmrMNcSnOgxfo_WLbanG5pOsqqtWctjRgtk1aw,1073
 CHAP/pipeline.py,sha256=nEoMJVn7ckn_hbo_O-B53tN-zo7MRZqcJsSlYWNbxNM,7358
 CHAP/processor.py,sha256=nqg1uK5jvADl35xuR6VIdU5uVGFVt-rzivnaZyOWruA,2639
 CHAP/reader.py,sha256=wGzAl_p5UnR7fC7Cie29S7RZTFFLcdOuhbViNDzH-4s,2534
 CHAP/runner.py,sha256=VdmCVA7wosGGI6QKJIAPuU1NFBMTCKPh1I1YZCR1qDc,6542
 CHAP/server.py,sha256=JAh5a7ZPh_Vx7fm0uI_g2WHLVxLn8s1uwBX8oMJ3G9c,3648
 CHAP/writer.py,sha256=9hed3_51AwSSH3kNisMR6Wq6mLInNGpgktPG5G_s-DM,2589
-CHAP/common/__init__.py,sha256=04js4qR7LriYbMfi0FBQ8o9NhQu0VkO0i7ubQPNF-6c,944
-CHAP/common/processor.py,sha256=ZIeJrSdnzBmrRvt692LOSEXqg6gj2xfGoBhqyAP8oPQ,25556
-CHAP/common/reader.py,sha256=sg9sMzwM6lDEqR9WSJblrULFX1ZB-euit6pJnBOkTD8,12406
-CHAP/common/writer.py,sha256=AuE5gJ5nzQ1hc1-5owwmdC18tMj0TLO2p6ZuA2NPGCA,10049
+CHAP/common/__init__.py,sha256=xNKfvDLBW3NIKqcjCMH7LAl__I43BKwKFQRGn_Sei0c,1033
+CHAP/common/processor.py,sha256=RJu-gGhY--cqmpJUQMaT3HW8MwdnFKk-sdQQ0I2FSsg,29183
+CHAP/common/reader.py,sha256=iVlOluctVpfMTKQzI79bwuaXKqAwU6XJ52oZSqKf7-E,13557
+CHAP/common/writer.py,sha256=Zk_LnYOwX-UwmlMAEwLbX3rmBooDGNV1O2o-lOxr2iQ,12242
 CHAP/common/models/__init__.py,sha256=MpmtY6biXgC7AaedznoSqFJJZ54YU8tBPgwzYJIVJ1c,200
 CHAP/common/models/integration.py,sha256=0WM2Q15XFQf-uydMALh3snbpoop-c5N6Pnf_O7ikXW0,27175
 CHAP/common/models/map.py,sha256=YIDojY_bgXS4k4GFOpmzo__yi7IsXl1mCIquTBS5srA,38280
@@ -32,23 +32,23 @@ CHAP/sin2psi/processor.py,sha256=6ytGpsK5u6tyUTzOJqAlcRdaimA4QfXZ6xpwGf2QMFo,97
 CHAP/sin2psi/reader.py,sha256=O0KeZcqACsZ8ngrliPU6I3u8SeQT0Aq866jCTbruXqc,94
 CHAP/sin2psi/writer.py,sha256=Y1CXWMRU87XeeDp4g4-sUgPP2UbCguYZUR_Cg5Ci6l8,94
 CHAP/tomo/__init__.py,sha256=7cwm1ufJkDKqrp2OPH_z7tKAOQ0S_RJbNainK0soKNo,328
-CHAP/tomo/models.py,sha256=zYmADnAIevO2B_yE1K8M3Dq2dT_Ed9oRtrXfC0ygsKg,7799
-CHAP/tomo/processor.py,sha256=W6CPyZ3znf78hIgj-iArI36jQq-56GC_el1c80hD_pI,142090
+CHAP/tomo/models.py,sha256=UPmn5rJl1MQe2cifBIOu7yBQO2qMmUtFu-KKw8XBMys,7889
+CHAP/tomo/processor.py,sha256=evNtZ3yTPKWDsm-RNxcQm7Pw7ERnwwDZu74QOqVrIAI,153325
 CHAP/tomo/reader.py,sha256=7nNP_KyIR-ghrrajCR2k5IsJnrLm6BIy-eAXIDXrQe8,123
 CHAP/tomo/writer.py,sha256=J7q_nmsqi_zbgAS-LvAciiBqtYD8hHJ4QmwS2oZAM2Q,123
 CHAP/utils/__init__.py,sha256=3blWv3cFKA4woMNUUI8d1WZFc4izlgMbfUPNAyBDiRs,183
 CHAP/utils/fit.py,sha256=VEhqAkNqkDpjBQ_kbOfGlNCEwmaPCh8RBc5SxHUy-OM,127878
-CHAP/utils/general.py,sha256=m8RyF5ZK-HgSd-K_IdOOa4x0AMh4wLkvNawCB9DYDl4,66955
+CHAP/utils/general.py,sha256=E1aKdoIEZCIDJoFGmOqSn0rRRA1rfbpImCmzhhyRGfY,67565
 CHAP/utils/material.py,sha256=NnLHAin3PrDxZiG6of8v7vFma0nAeOIRZJuXxSN_xj8,11495
 CHAP/utils/parfile.py,sha256=GxBWG6EVKQnV1I_r_m4nfJrCb0VGAn6tjEfuxVTg-aA,7227
-CHAP/utils/scanparsers.py,sha256=PAyhB9MWDd61zgU7BNeJhWSmvvWfo0ExxRnhKUzUj3U,43927
+CHAP/utils/scanparsers.py,sha256=zCyad4P6OTytozM-rJjmIKXrOqeotbUHmr8Xc4YhpG8,44881
 MLaaS/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 MLaaS/ktrain.py,sha256=SPDUOQgjBDSx7sI8vZNXog9orvSyKmzpe6TdGHol9qM,7467
 MLaaS/mnist_img.py,sha256=ppDtlo6yrNQy0oIhFZVOnLvHJrR3ZPZ3PjZTtJY8l0E,2738
 MLaaS/tfaas_client.py,sha256=zpZ201wwcQBW1XkzDakD9Kl_NRSESAUdbnN6k6Ey15A,14889
-ChessAnalysisPipeline-0.0.12.dist-info/LICENSE,sha256=GrJL25aZivxje_x-zBbeWASvdmgztxv8kBMhIP4XSMo,1075
-ChessAnalysisPipeline-0.0.12.dist-info/METADATA,sha256=k_0KsJROERCMKLjL-n6CWWujII_QvFmiqXIAijRfqKg,1542
-ChessAnalysisPipeline-0.0.12.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
-ChessAnalysisPipeline-0.0.12.dist-info/entry_points.txt,sha256=w-KIKdUjmj5GCobrFC4_jexCsFB4yMXYjrsMWrhI6Co,42
-ChessAnalysisPipeline-0.0.12.dist-info/top_level.txt,sha256=BKhggOWLb9dD6oQm1RXrkJPnXm-zJxVzQef1iXYtt2k,11
-ChessAnalysisPipeline-0.0.12.dist-info/RECORD,,
+ChessAnalysisPipeline-0.0.13.dist-info/LICENSE,sha256=GrJL25aZivxje_x-zBbeWASvdmgztxv8kBMhIP4XSMo,1075
+ChessAnalysisPipeline-0.0.13.dist-info/METADATA,sha256=KTZzy22v8P2ISFOgRLCXMDc6ytFoR2yayPtficwLHZA,1542
+ChessAnalysisPipeline-0.0.13.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+ChessAnalysisPipeline-0.0.13.dist-info/entry_points.txt,sha256=w-KIKdUjmj5GCobrFC4_jexCsFB4yMXYjrsMWrhI6Co,42
+ChessAnalysisPipeline-0.0.13.dist-info/top_level.txt,sha256=BKhggOWLb9dD6oQm1RXrkJPnXm-zJxVzQef1iXYtt2k,11
+ChessAnalysisPipeline-0.0.13.dist-info/RECORD,,

{ChessAnalysisPipeline-0.0.12.dist-info → ChessAnalysisPipeline-0.0.13.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.2)
+Generator: bdist_wheel (0.42.0)
 Root-Is-Purelib: true
 Tag: py3-none-any