ChessAnalysisPipeline 0.0.4__py3-none-any.whl → 0.0.5__py3-none-any.whl

CHAP/common/models/__init__.py

@@ -1,2 +0,0 @@
-from CHAP.common.models.map import MapConfig
-from CHAP.common.models.integration import IntegrationConfig

CHAP/common/processor.py

@@ -127,8 +127,8 @@ class IntegrateMapProcessor(Processor):
         self.logger.debug('Getting configuration objects')
         t0 = time()
 
-        from CHAP.common.models import MapConfig
-        from CHAP.common.models import IntegrationConfig
+        from CHAP.common.models.map import MapConfig
+        from CHAP.common.models.integration import IntegrationConfig
 
         map_config = False
         integration_config = False

CHAP/common/utils/__init__.py

@@ -1,37 +0,0 @@
-from CHAP.common.utils.fit import (Fit,
-                                   FitMap,
-                                   FitMultipeak)
-from CHAP.common.utils.material import Material
-
-# def create_mask(data, bounds, exclude_bounds=True, current_mask=None):
-#     '''Return a boolean array that masks out the values in `bounds` when applied
-#     to `data`.
-
-#     :param data: the array for which a mask will be constructed
-#     :type data: Union[list, numpy.ndarray]
-#     :param bounds: a range of values in `data` (min, max) that the mask will
-#         exclude (or include if `exclude_bounds=False`).
-#     :type bounds: tuple
-#     :param exclude_bounds: should applying the mask to `data`  exclude (`True`)
-#         or include (`False`) the value ranges in `bounds`, defaults to `True`
-#     :type exclude_bounds: True, optional
-#     :param current_mask: an existing mask array for `data` that will be "or"-ed
-#         with the mask constructed from `bounds` before returning, defaults to
-#         None
-#     :type current_mask: numpy.ndarray(dtype=numpy.bool_), optional
-#     :return: a boolean mask array for `data`.
-#     :rtype: numpy.ndarray(dtype=numpy.bool_)
-#     '''
-
-#     import numpy as np
-
-#     min_, max_ = bounds
-#     if exclude_bounds:
-#         mask = np.logical_or(data < min_, data > max_)
-#     else:
-#         mask = np.logical_and(data > min_, data < max_)
-
-#     if current_mask is not None:
-#         mask = np.logical_or(mask, current_mask)
-
-#     return(mask)

CHAP/edd/models.py

@@ -154,13 +154,13 @@ class MCACeriaCalibrationConfig(BaseModel):
         return(interpolation_function)
 
     def material(self):
-        '''Get CeO2 as a `CHAP.common.utils.Material` object.
+        '''Get CeO2 as a `CHAP.common.utils.material.Material` object.
 
         :return: CeO2 material
-        :rtype: CHAP.common.utils.Material
+        :rtype: CHAP.common.utils.material.Material
         '''
 
-        from CHAP.common.utils import Material
+        from CHAP.common.utils.material import Material
         material = Material(material_name=self.hexrd_h5_material_name,
                             material_file=self.hexrd_h5_material_file,
                             lattice_parameters_angstroms=self.lattice_parameter_angstrom)

CHAP/edd/processor.py

@@ -83,7 +83,7 @@ class MCACeriaCalibrationProcessor(Processor):
         :rtype: float, float, float
         '''
 
-        from CHAP.common.utils import Fit, FitMultipeak
+        from CHAP.common.utils.fit import Fit, FitMultipeak
         import numpy as np
         from scipy.constants import physical_constants
 
@@ -127,7 +127,8 @@ class MCACeriaCalibrationProcessor(Processor):
                     fit_mca_intensities,
                     fit_E0,
                     x=fit_mca_energies,
-                    fit_type='uniform')
+                    fit_type='uniform',
+                    plot=False)
 
             # Extract values of interest from the best values for the uniform fit
             # parameters
@@ -149,7 +150,8 @@ class MCACeriaCalibrationProcessor(Processor):
                     fit_mca_intensities,
                     uniform_fit_centers,
                     x=fit_mca_energies,
-                    fit_type='unconstrained')
+                    fit_type='unconstrained',
+                    plot=False)
 
             # Extract values of interest from the best values for the
             # unconstrained fit parameters
@@ -224,7 +226,7 @@ class MCADataProcessor(Processor):
         :rtype: tuple[MapConfig, MCACeriaCalibrationConfig]
         '''
 
-        from CHAP.common.models import MapConfig
+        from CHAP.common.models.map import MapConfig
         from CHAP.edd.models import MCACeriaCalibrationConfig
 
         map_config = False

CHAP/tomo/processor.py

@@ -117,7 +117,7 @@ class TomoDataProcessor(Processor):
         :rtype: dict
         '''
         #:rtype: dict{'map': MapConfig, 'reduce': TomoReduceConfig} RV: Is there a way to denote optional items?
-        from CHAP.common.models import MapConfig
+        from CHAP.common.models.map import MapConfig
         from CHAP.tomo.models import TomoSetupConfig, TomoReduceConfig, TomoFindCenterConfig, \
                 TomoReconstructConfig, TomoCombineConfig
         from nexusformat.nexus import NXroot
@@ -550,8 +550,6 @@ class Tomo:
             nxentry = data[data.attrs['default']]
         else:
             raise ValueError(f'Invalid parameter data ({data})')
-        if 'data' in nxentry:
-            del nxentry['data']
 
         # Create an NXprocess to store data reduction (meta)data
         reduced_data = NXprocess()

{ChessAnalysisPipeline-0.0.4.dist-info → ChessAnalysisPipeline-0.0.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ChessAnalysisPipeline
-Version: 0.0.4
+Version: 0.0.5
 Summary: CHESS analysis pipeline framework
 Home-page: https://github.com/CHESSComputing/ChessAnalysisPipeline
 Author: Keara Soloway, Rolf Verberg, Valentin Kuznetsov

{ChessAnalysisPipeline-0.0.4.dist-info → ChessAnalysisPipeline-0.0.5.dist-info}/RECORD

@@ -5,20 +5,20 @@ CHAP/reader.py,sha256=12Xn78J06KJ5wzGnCZKSiak8irCtOVX2wtxV7eH3Pb0,3577
 CHAP/runner.py,sha256=MA0Q3KTAnPnw25i1L7XPs4ZkszfRfByD_qBshsokL2A,2412
 CHAP/writer.py,sha256=tDeQIEgTm-p8zH0g8EmqFTiGBFRM_A_Q9PyBjE1vaac,2759
 CHAP/common/__init__.py,sha256=cnkVDvaf3NhnmBAzwuUFpotYv9VWxOVhKwqE0qZLbNQ,991
-CHAP/common/processor.py,sha256=sEiSFqXhskrKVV6BDwGFwWpbAJ0aV1JXz2BO1l3oql4,24425
+CHAP/common/processor.py,sha256=nKut7GfBLZmp7QCg9NRIzVMBDbrIYOIPKQ182w-Dn28,24441
 CHAP/common/reader.py,sha256=DqKRLfG5PLf2aj039aV2FIN5ZmhR7XkZ6EyPDSLUZqY,3547
 CHAP/common/writer.py,sha256=HwMMCVldjQGb3HK9ysfdyfkUplnrdZjyqHnon0ne3DU,2910
-CHAP/common/models/__init__.py,sha256=wkCmQ08zciMzjbQVBjKZacSPUGICqTFcfJ3VaWYBtNY,106
+CHAP/common/models/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 CHAP/common/models/integration.py,sha256=q18QpPtI7iLd1Asj3NnKbHmB5YIlLm9crKPmtLT37c0,25169
 CHAP/common/models/map.py,sha256=OXtXhohGrKrPCgkvxrweSDxnYpJf39KXxvvYsE5JBTo,25035
-CHAP/common/utils/__init__.py,sha256=lDyThufb9FjaqtUnZ7vDEyaF0r9S5Wo5Ty4qkjYNZRY,1497
+CHAP/common/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 CHAP/common/utils/fit.py,sha256=-nOPfd6yUnUDNyLjLGJVxOp0ET4fKD-Bwh5C_bLx8bY,127303
 CHAP/common/utils/general.py,sha256=VkGFECXdbB2NicOt9iGhpIJPdvGPc6eHdtiaiqzDM1A,48178
 CHAP/common/utils/material.py,sha256=KQfORTqLbp8p9pWeSYD6mYzzpYncIEfbHVPiZ5E1PrA,10472
 CHAP/common/utils/scanparsers.py,sha256=ZxFgMQrD98vTjXbkqPXpA_xjWhL7Gk0cIBD0mvf67GQ,34386
 CHAP/edd/__init__.py,sha256=0POOQcuL72QQJghdN9LfYHNZCHdAOjYaLYg2ebr_URo,262
-CHAP/edd/models.py,sha256=E3gUBI0bgnR_GoLJE5XkY8bOWs7z44dcK0QaqqP0vXU,8448
-CHAP/edd/processor.py,sha256=AjI9CZyzBDgBNzKb72n1sc_dkH60LY0h5SyXTkTPbUo,13557
+CHAP/edd/models.py,sha256=EmJnaHMes3JXGoYqItMB0-cMmLma_GfhBCpRlj5fLmw,8475
+CHAP/edd/processor.py,sha256=ltbgBmegBOV_RrSi30bhufUKfaeZDAYp1SO8iR5i1sw,13629
 CHAP/edd/reader.py,sha256=md3gt82kjNOR3mMjcsCfqbmWLuPhl6JA6Qk1ek9tItA,96
 CHAP/edd/writer.py,sha256=jQGikOjYx7-MURPqMkDqYw8sig2HauGulUlH1nf-jvY,96
 CHAP/inference/__init__.py,sha256=huci54T9WyoORENtAO-Wq7qdKfQvh8ocaRwOAoov2fo,129
@@ -35,16 +35,16 @@ CHAP/sin2psi/reader.py,sha256=md3gt82kjNOR3mMjcsCfqbmWLuPhl6JA6Qk1ek9tItA,96
 CHAP/sin2psi/writer.py,sha256=jQGikOjYx7-MURPqMkDqYw8sig2HauGulUlH1nf-jvY,96
 CHAP/tomo/__init__.py,sha256=cFq3uemguYhC3y2hKAO60Omoll5p8mWBHdCrCjBWfCA,150
 CHAP/tomo/models.py,sha256=8-sFRVfbMyy-R0p3HdNaJXH1K9YKDgb4JEXehPYuRns,4857
-CHAP/tomo/processor.py,sha256=_TILlIyM4-dy18CTmqJ0xF-MR0x3RKwppW1mt_dcqV0,97527
+CHAP/tomo/processor.py,sha256=PdmZ30YrGz3pOI0Twp-F4xoaqK6ZKwxKdF74AWWvQ5c,97469
 CHAP/tomo/reader.py,sha256=md3gt82kjNOR3mMjcsCfqbmWLuPhl6JA6Qk1ek9tItA,96
 CHAP/tomo/writer.py,sha256=jQGikOjYx7-MURPqMkDqYw8sig2HauGulUlH1nf-jvY,96
 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-0.0.4.dist-info/LICENSE,sha256=GrJL25aZivxje_x-zBbeWASvdmgztxv8kBMhIP4XSMo,1075
-ChessAnalysisPipeline-0.0.4.dist-info/METADATA,sha256=KzNtqjPNZkHL92ukFXnF96tA2wv8xvEL5XDKdp-XafM,1219
-ChessAnalysisPipeline-0.0.4.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
-ChessAnalysisPipeline-0.0.4.dist-info/entry_points.txt,sha256=w-KIKdUjmj5GCobrFC4_jexCsFB4yMXYjrsMWrhI6Co,42
-ChessAnalysisPipeline-0.0.4.dist-info/top_level.txt,sha256=BKhggOWLb9dD6oQm1RXrkJPnXm-zJxVzQef1iXYtt2k,11
-ChessAnalysisPipeline-0.0.4.dist-info/RECORD,,
+ChessAnalysisPipeline-0.0.5.dist-info/LICENSE,sha256=GrJL25aZivxje_x-zBbeWASvdmgztxv8kBMhIP4XSMo,1075
+ChessAnalysisPipeline-0.0.5.dist-info/METADATA,sha256=wC6KLzGsoNAxz7UZEH19pHCowdOjg3Ezt_k86RZTFa8,1219
+ChessAnalysisPipeline-0.0.5.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
+ChessAnalysisPipeline-0.0.5.dist-info/entry_points.txt,sha256=w-KIKdUjmj5GCobrFC4_jexCsFB4yMXYjrsMWrhI6Co,42
+ChessAnalysisPipeline-0.0.5.dist-info/top_level.txt,sha256=BKhggOWLb9dD6oQm1RXrkJPnXm-zJxVzQef1iXYtt2k,11
+ChessAnalysisPipeline-0.0.5.dist-info/RECORD,,