ChessAnalysisPipeline 0.0.13__py3-none-any.whl → 0.0.14__py3-none-any.whl

CHAP/utils/scanparsers.py

@@ -15,6 +15,9 @@ import numpy as np
 from pyspec.file.spec import FileSpec
 from pyspec.file.tiff import TiffFile
 
+@cache
+def filespec(spec_file_name):
+    return FileSpec(spec_file_name)
 
 class ScanParser:
     """Partial implementation of a class representing a SPEC scan and
@@ -64,7 +67,7 @@ class ScanParser:
         # NB This FileSpec instance is not stored as a private
         # attribute because it cannot be pickled (and therefore could
         # cause problems for parallel code that uses ScanParsers).
-        return FileSpec(self.spec_file_name)
+        return filespec(self.spec_file_name)
 
     @property
     def scan_path(self):
@@ -323,6 +326,10 @@ class SMBScanParser(ScanParser):
         json_files = fnmatch_filter(
             os.listdir(self.scan_path),
             f'{self._par_file_pattern}.json')
+        if not json_files:
+            json_files = fnmatch_filter(
+                os.listdir(self.scan_path),
+                f'*.json')
         if len(json_files) != 1:
             raise RuntimeError(f'{self.scan_title}: cannot find the '
                                '.json file to decode the .par file')
@@ -336,15 +343,19 @@ class SMBScanParser(ScanParser):
             raise RuntimeError(f'{self.scan_title}: cannot find scan pars '
                                'without a "SCAN_N" column in the par file')
 
-        par_files = fnmatch_filter(
-            os.listdir(self.scan_path),
-            f'{self._par_file_pattern}.par')
-        if len(par_files) != 1:
-            raise RuntimeError(f'{self.scan_title}: cannot find the .par '
-                               'file for this scan directory')
+        if hasattr(self, '_par_file'):
+            par_file = self._par_file
+        else:
+            par_files = fnmatch_filter(
+                os.listdir(self.scan_path),
+                f'{self._par_file_pattern}.par')
+            if len(par_files) != 1:
+                raise RuntimeError(f'{self.scan_title}: cannot find the .par '
+                                   'file for this scan directory')
+            par_file = os.path.join(self.scan_path, par_files[0])
         par_dict = None
-        with open(os.path.join(self.scan_path, par_files[0])) as par_file:
-            par_reader = reader(par_file, delimiter=' ')
+        with open(par_file) as f:
+            par_reader = reader(f, delimiter=' ')
             for row in par_reader:
                 if len(row) == len(par_col_names):
                     row_scann = int(row[scann_col_idx])
@@ -531,7 +542,7 @@ class FMBLinearScanParser(LinearScanParser, FMBScanParser):
     """
 
     def get_spec_scan_motor_mnes(self):
-        if self.spec_macro == 'flymesh':
+        if self.spec_macro in ('flymesh', 'mesh', 'flydmesh', 'dmesh'):
             m1_mne = self.spec_args[0]
             try:
                 # Try post-summer-2022 format
@@ -551,7 +562,7 @@ class FMBLinearScanParser(LinearScanParser, FMBScanParser):
                            f'for scans of type {self.spec_macro}')
 
     def get_spec_scan_motor_vals(self):
-        if self.spec_macro == 'flymesh':
+        if self.spec_macro in ('flymesh', 'mesh', 'flydmesh', 'dmesh'):
             m1_start = float(self.spec_args[1])
             m1_end = float(self.spec_args[2])
             m1_npt = int(self.spec_args[3]) + 1
@@ -584,7 +595,7 @@ class FMBLinearScanParser(LinearScanParser, FMBScanParser):
                            f'for scans of type {self.spec_macro}')
 
     def get_spec_scan_shape(self):
-        if self.spec_macro == 'flymesh':
+        if self.spec_macro in ('flymesh', 'mesh', 'flydmesh', 'dmesh'):
             fast_mot_npts = int(self.spec_args[3]) + 1
             try:
                 # Try post-summer-2022 format
@@ -605,7 +616,7 @@ class FMBLinearScanParser(LinearScanParser, FMBScanParser):
                            f'for scans of type {self.spec_macro}')
 
     def get_spec_scan_dwell(self):
-        if self.macro == 'flymesh':
+        if self.macro in ('flymesh', 'mesh', 'flydmesh', 'dmesh'):
             try:
                 # Try post-summer-2022 format
                 dwell = float(self.spec_args[4])
@@ -704,7 +715,15 @@ class SMBLinearScanParser(LinearScanParser, SMBScanParser):
     """
 
     def get_spec_scan_dwell(self):
-        if self.spec_macro in ('flymesh', 'flyscan', 'ascan'):
+        if self.spec_macro in ('flymesh', 'mesh'):
+            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 == 'tseries':
             return float(self.spec_args[1])
@@ -714,8 +733,18 @@ class SMBLinearScanParser(LinearScanParser, SMBScanParser):
                            f'for scans of type {self.spec_macro}')
 
     def get_spec_scan_motor_mnes(self):
-        if self.spec_macro == 'flymesh':
-            return (self.spec_args[0], self.spec_args[5])
+        if self.spec_macro in ('flymesh', 'mesh'):
+            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'):
@@ -724,13 +753,27 @@ class SMBLinearScanParser(LinearScanParser, SMBScanParser):
                            f'for scans of type {self.spec_macro}')
 
     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)
+        if self.spec_macro in ('flymesh', 'mesh'):
+            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]),
@@ -738,31 +781,31 @@ class SMBLinearScanParser(LinearScanParser, SMBScanParser):
                                    int(self.spec_args[3])+1)
             return (mot_vals,)
         if self.spec_macro in ('tseries', 'loopscan'):
-            return self.spec_scan.data[:,0]
+            return (self.spec_scan.data[:,0],)
         raise RuntimeError(f'{self.scan_title}: cannot determine scan motors '
                            f'for scans of type {self.spec_macro}')
 
     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
+        if self.spec_macro in ('flymesh', 'mesh'):
+            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
             return (mot_npts,)
         if self.spec_macro in ('tseries', 'loopscan'):
-            return len(np.array(self.spec_scan.data[:,0]))
+            return (len(np.array(self.spec_scan.data[:,0])),)
         raise RuntimeError(f'{self.scan_title}: cannot determine scan shape '
                            f'for scans of type {self.spec_macro}')
 
-    def get_spec_scan_dwell(self):
-        if self.spec_macro == 'flymesh':
-            return float(self.spec_args[4])
-        if self.spec_macro in ('flyscan', 'ascan'):
-            return float(self.spec_args[-1])
-        raise RuntimeError(f'{self.scan_title}: cannot determine dwell time '
-                           f'for scans of type {self.spec_macro}')
-
     def get_detector_data_path(self):
         return os.path.join(self.scan_path, str(self.scan_number))
 
@@ -963,12 +1006,14 @@ class SMBRotationScanParser(RotationScanParser, SMBScanParser):
     with the typical tomography setup at SMB.
     """
 
-    def __init__(self, spec_file_name, scan_number):
+    def __init__(self, spec_file_name, scan_number, par_file=None):
         self._scan_type = None
         super().__init__(spec_file_name, scan_number)
 
         self._katefix = 0  # RV remove when no longer needed
         self._par_file_pattern = f'id*-*tomo*-{self.scan_name}'
+        if par_file is not None:
+            self._par_file = par_file
 
     @property
     def scan_type(self):
@@ -1038,7 +1083,8 @@ class SMBRotationScanParser(RotationScanParser, SMBScanParser):
         if os.path.isfile(file_name_full):
             return file_name_full
         raise RuntimeError(f'{self.scan_title}: could not find detector image '
-                           f'file for scan step ({scan_step_index})')
+                           f'file ({file_name_full}) for scan step '
+                           f'({scan_step_index})')
 
     def get_detector_data(self, detector_prefix, scan_step_index=None):
         if scan_step_index is None:
@@ -1090,10 +1136,66 @@ class SMBMCAScanParser(MCAScanParser, SMBLinearScanParser):
     """Concrete implementation of a class representing a scan taken
     with the typical EDD setup at SMB or FAST.
     """
+    detector_data_formats = ('spec', 'h5')
+    def __init__(self, spec_file_name, scan_number, detector_data_format=None):
+        """Constructor for SMBMCAScnaParser.
+
+        :param spec_file: Path to scan's SPEC file
+        :type spec_file: str
+        :param scan_number: Number of the SPEC scan
+        :type scan_number: int
+        :param detector_data_format: Format of the MCA data collected,
+            defaults to None
+        :type detector_data_format: Optional[Literal["spec", "h5"]]
+        """
+        super().__init__(spec_file_name, scan_number)
 
-    def get_detector_num_bins(self, detector_prefix):
-        with open(self.get_detector_data_file(detector_prefix)) \
-             as detector_file:
+        self.detector_data_format = None
+        if detector_data_format is None:
+            self.init_detector_data_format()
+        else:
+            if detector_data_format.lower() in self.detector_data_formats:
+                self.detector_data_format = detector_data_format.lower()
+            else:
+                raise ValueError(
+                    'Unrecognized value for detector_data_format: '
+                    + f'{detector_data_format}. Allowed values are: '
+                    + ', '.join(self.detector_data_formats))
+
+    def init_detector_data_format(self):
+        """Determine and set a value for the instance variable
+        `detector_data_format` based on the presence / absence of
+        detector data files of different formats conventionally
+        associated with this scan. Also set the corresponding
+        appropriate value for `_detector_data_path`.
+        """
+        try:
+            self._detector_data_path = self.scan_path
+            detector_file = self.get_detector_data_file_spec()
+        except OSError:
+            try:
+                self._detector_data_path = os.path.join(
+                    self.scan_path, str(self.scan_number), 'edd')
+                detector_file = self.get_detector_data_file_h5()
+            except OSError:
+                raise RuntimeError(
+                    f"{self.scan_title}: Can't determine detector data format")
+            else:
+                self.detector_data_format = 'h5'
+        else:
+            self.detector_data_format = 'spec'
+
+    def get_detector_data_path(self):
+        raise NotImplementedError
+
+    def get_detector_num_bins(self, element_index=0):
+        if self.detector_data_format == 'spec':
+            return self.get_detector_num_bins_spec()
+        elif self.detector_data_format == 'h5':
+            return self.get_detector_num_bins_h5(element_index)
+
+    def get_detector_num_bins_spec(self):
+        with open(self.get_detector_data_file_spec()) as detector_file:
             lines = detector_file.readlines()
         for line in lines:
             if line.startswith('#@CHANN'):
@@ -1103,33 +1205,101 @@ class SMBMCAScanParser(MCAScanParser, SMBLinearScanParser):
                     return int(number_saved)
                 except:
                     continue
-        raise RuntimeError(f'{self.scan_title}: could not find num_bins for '
-                           f'detector {detector_prefix}')
+        raise RuntimeError(f'{self.scan_title}: could not find num_bins')
 
-    def get_detector_data_path(self):
-        return self.scan_path
-
-    def get_detector_data_file(self, detector_prefix, scan_step_index=0):
+    def get_detector_num_bins_h5(self, element_index):
+        from h5py import File
+        detector_file = self.get_detector_data_file_h5()
+        with File(detector_file) as h5_file:
+            dset_shape = h5_file['/entry/data/data'].shape
+        return dset_shape[-1]
+
+    def get_detector_data_file(self, scan_step_index=0):
+        if self.detector_data_format == 'spec':
+            return self.get_detector_data_file_spec()
+        elif self.detector_data_format == 'h5':
+            return self.get_detector_data_file_h5(
+                scan_step_index=scan_step_index)
+
+    def get_detector_data_file_spec(self):
+        """Return the filename (full absolute path) to the file
+        containing spec-formatted MCA data for this scan.
+        """
         file_name = f'spec.log.scan{self.scan_number}.mca1.mca'
         file_name_full = os.path.join(self.detector_data_path, file_name)
         if os.path.isfile(file_name_full):
             return file_name_full
-        raise RuntimeError(
-            f'{self.scan_title}: could not find detector image file')
+        raise OSError(
+            '{self.scan_title}: could not find detector image file'
+        )
+
+    def get_detector_data_file_h5(self, scan_step_index=0):
+        """Return the filename (full absolute path) to the file
+        containing h5-formatted MCA data for this scan.
+
+        :param scan_step_index:
+        """
+        scan_step = self.get_scan_step(scan_step_index)
+        if len(self.spec_scan_shape) == 1:
+            filename_index = 0
+        elif len(self.spec_scan_shape) == 2:
+            scan_step = self.get_scan_step(scan_step_index)
+            filename_index = scan_step[0]
+        else:
+            raise NotImplementedError(
+                'Cannot find detector file for scans with dimension > 2')
+        file_name = list_smb_mca_detector_files_h5(
+            self.detector_data_path)[filename_index]
+        file_name_full = os.path.join(self.detector_data_path, file_name)
+        if os.path.isfile(file_name_full):
+            return file_name_full
+        raise OSError(
+            '{self.scan_title}: could not find detector image file'
+        )
+
+
+    def get_all_detector_data(self, detector):
+        """Return a 2D array of all MCA spectra collected in this scan
+        by the detector element indicated with `detector`.
 
-    def get_all_detector_data(self, detector_prefix):
+        :param detector: For detector data collected in SPEC format,
+            this is the detector prefix as it appears in the spec MCA
+            data file. For detector data collected in H5 format, this
+            is the index of a particular detector element.
+        :type detector: Union[str, int]
+        :rtype: numpy.ndarray
+        """
+        if self.detector_data_format == 'spec':
+            return self.get_all_detector_data_spec(detector)
+        elif self.detector_data_format == 'h5':
+            try:
+                element_index = int(detector)
+            except:
+                raise TypeError(f'{detector} is not an integer element index')
+            return self.get_all_detector_data_h5(element_index)
+
+    def get_all_detector_data_spec(self, detector_prefix):
+        """Return a 2D array of all MCA spectra collected by a
+        detector in the spec MCA file format during the scan.
+
+        :param detector_prefix: Detector name at is appears in the
+            spec MCA file.
+        :type detector_prefix: str
+        :returns: 2D array of MCA spectra
+        :rtype: numpy.ndarray
+        """
         # This should be easy with pyspec, but there are bugs in
         # pyspec for MCA data.....  or is the 'bug' from a nonstandard
         # implementation of some macro on our end?  According to spec
         # manual and pyspec code, mca data should always begin w/ '@A'
-        # In example scans, it begins with '@mca1' instead
+        # In example scans, it begins with '@{detector_prefix}'
+        # instead
         data = []
 
-        with open(self.get_detector_data_file(detector_prefix)) \
-                as detector_file:
+        with open(self.get_detector_data_file_spec()) as detector_file:
             lines = [line.strip("\\\n") for line in detector_file.readlines()]
 
-        num_bins = self.get_detector_num_bins(detector_prefix)
+        num_bins = self.get_detector_num_bins()
 
         counter = 0
         for line in lines:
@@ -1156,6 +1326,106 @@ class SMBMCAScanParser(MCAScanParser, SMBLinearScanParser):
 
         return np.array(data)
 
-    def get_detector_data(self, detector_prefix, scan_step_index:int):
-        detector_data = self.get_all_detector_data(detector_prefix)
+    def get_all_detector_data_h5(self, element_index):
+        """Return a 2D array of all MCA spectra collected by a
+        detector in the h5 file format during the scan.
+
+        :param element_index: The index of a particualr MCA element to
+            return data for.
+        :type element_index: int
+        :returns: 2D array of MCA spectra
+        :rtype: numpy.ndarray
+        """
+        detector_data = np.empty(
+            (self.spec_scan_npts,
+             self.get_detector_num_bins_h5(element_index)))
+        detector_files = list_smb_mca_detector_files_h5(
+            self.detector_data_path)
+        for i, detector_file in enumerate(detector_files):
+            full_filename = os.path.join(
+                self.detector_data_path, detector_file)
+            element_data = get_all_mca_data_h5(
+                full_filename)[:,element_index,:]
+            i_0 = i * self.spec_scan_shape[0]
+            if len(self.spec_scan_shape) == 2:
+                i_f = i_0 + self.spec_scan_shape[1]
+            else:
+                i_f = self.spec_scan_npts
+            detector_data[i_0:i_f] = element_data
+        return detector_data
+
+    def get_detector_data(self, detector, scan_step_index:int):
+        """Return a single MCA spectrum for the detector indicated.
+
+        :param detector: If this scan collected MCA data in "spec"
+            format, this is the detector prefix as it appears in the
+            spec MCA data file. If this scan collected data in .h5
+            format, this is the index of the detector element of
+            interest.:type detector: typing.Union[str, int]
+        :param scan_step_index: Index of the scan step to return the
+            spectrum from.
+        :type scan_step_index: int
+        :returns: A single MCA spectrum
+        :rtype: numpy.ndarray
+        """
+        detector_data = self.get_all_detector_data(detector)
         return detector_data[scan_step_index]
+
+@cache
+def list_smb_mca_detector_files_h5(detector_data_path):
+    """Return a sorted list of all *.hdf5 files in a directory
+
+    :param detector_data_path: Directory to return *.hdf5 files from
+    :type detector_data_path: str
+    :returns: Sorted list of detector data filenames
+    :rtype: list[str]
+    """
+    return sorted(
+        [f for f in os.listdir(detector_data_path) if f.endswith('.hdf5')])
+
+@cache
+def get_all_mca_data_h5(filename):
+    """Return all data from all elements from an MCA data file
+
+    :param filename: Name of the MCA h5 data file
+    :type filename: str
+    :returns: 3D array of MCA spectra where the first axis is scan
+        step, second index is detector element, third index is channel
+        energy.
+    :rtype: numpy.ndarray
+    """
+    import os
+
+    from h5py import File
+    import numpy as np
+
+    with File(filename) as h5_file:
+        data = h5_file['/entry/data/data'][:]
+
+    # Prior to 2023-12-12, there was an issue where the XPS23 detector
+    # was capturing one or two frames of all 0s at the start of the
+    # dataset in every hdf5 file. In both cases, there is only ONE
+    # extra frame of data relative to the number of frames that should
+    # be there (based on the number of points in the spec scan). If
+    # one frame of all 0s is present: skip it and deliver only the
+    # real data. If two frames of all 0s are present: detector data
+    # will be missing for the LAST step in the scan. Skip the first
+    # two frames of all 0s in the hdf5 dataset, then add a frame of
+    # fake data (all 0-s) to the end of that real data so that the
+    # number of detector data frames matches the number of points in
+    # the spec scan.
+    check_zeros_before = 1702357200
+    file_mtime = os.path.getmtime(filename)
+    if file_mtime <= check_zeros_before:
+        if not np.any(data[0]):
+            # If present, remove first frame of blank data
+            print('Warning: removing blank first frame of detector data')
+            data = data[1:]
+            if not np.any(data[0]):
+                # If present, shift second frame of blank data to the
+                # end
+                print('Warning: shifting second frame of blank detector data '
+                      + 'to the end of the scan')
+                data = np.concatenate((data[1:], np.asarray([data[0]])))
+
+    return data

{ChessAnalysisPipeline-0.0.13.dist-info → ChessAnalysisPipeline-0.0.14.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ChessAnalysisPipeline
-Version: 0.0.13
+Version: 0.0.14
 Summary: CHESS analysis pipeline framework
 Home-page: https://github.com/CHESSComputing/ChessAnalysisPipeline
 Author: Keara Soloway, Rolf Verberg, Valentin Kuznetsov

{ChessAnalysisPipeline-0.0.13.dist-info → ChessAnalysisPipeline-0.0.14.dist-info}/RECORD

@@ -1,23 +1,23 @@
 CHAP/TaskManager.py,sha256=NEqg2jAq10kbScE18XtzY3liqkIdAtysaR-gMG5tBzs,6803
-CHAP/__init__.py,sha256=fgkAhLmrMNcSnOgxfo_WLbanG5pOsqqtWctjRgtk1aw,1073
-CHAP/pipeline.py,sha256=nEoMJVn7ckn_hbo_O-B53tN-zo7MRZqcJsSlYWNbxNM,7358
+CHAP/__init__.py,sha256=CjKQO1ao0OkBYJyBjtyt-kNq6PHBVlDPl65EvhyVGnw,1073
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 CHAP/processor.py,sha256=nqg1uK5jvADl35xuR6VIdU5uVGFVt-rzivnaZyOWruA,2639
 CHAP/reader.py,sha256=wGzAl_p5UnR7fC7Cie29S7RZTFFLcdOuhbViNDzH-4s,2534
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 CHAP/server.py,sha256=JAh5a7ZPh_Vx7fm0uI_g2WHLVxLn8s1uwBX8oMJ3G9c,3648
 CHAP/writer.py,sha256=9hed3_51AwSSH3kNisMR6Wq6mLInNGpgktPG5G_s-DM,2589
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 CHAP/common/models/__init__.py,sha256=MpmtY6biXgC7AaedznoSqFJJZ54YU8tBPgwzYJIVJ1c,200
 CHAP/common/models/integration.py,sha256=0WM2Q15XFQf-uydMALh3snbpoop-c5N6Pnf_O7ikXW0,27175
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-CHAP/edd/__init__.py,sha256=w3qmOjaoeiY69pf0ombi6TPRHcm60_T3sbTms5393pQ,422
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 CHAP/edd/reader.py,sha256=O0KeZcqACsZ8ngrliPU6I3u8SeQT0Aq866jCTbruXqc,94
-CHAP/edd/utils.py,sha256=9K_OnSUNcRL_oLDqivXkqbwbxE9HmP1cXf-6vkkPDxI,35095
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 CHAP/edd/writer.py,sha256=Y1CXWMRU87XeeDp4g4-sUgPP2UbCguYZUR_Cg5Ci6l8,94
 CHAP/inference/__init__.py,sha256=GwpEKEMHY1-3AE7HWKBdBz_i7N1sz7xwve6y9tZ7Skk,263
 CHAP/inference/processor.py,sha256=TYYPtZ3YlZS1kgvGr6I_9RvSaR0kn9PKL98A3QwqeDI,2065
@@ -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
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-CHAP/tomo/processor.py,sha256=evNtZ3yTPKWDsm-RNxcQm7Pw7ERnwwDZu74QOqVrIAI,153325
+CHAP/tomo/models.py,sha256=TTq1QbIK1h2xVpPWXwc41fWaDCavmufcTOK3N-MxGh0,8293
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 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
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 CHAP/utils/material.py,sha256=NnLHAin3PrDxZiG6of8v7vFma0nAeOIRZJuXxSN_xj8,11495
 CHAP/utils/parfile.py,sha256=GxBWG6EVKQnV1I_r_m4nfJrCb0VGAn6tjEfuxVTg-aA,7227
-CHAP/utils/scanparsers.py,sha256=zCyad4P6OTytozM-rJjmIKXrOqeotbUHmr8Xc4YhpG8,44881
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 MLaaS/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 MLaaS/ktrain.py,sha256=SPDUOQgjBDSx7sI8vZNXog9orvSyKmzpe6TdGHol9qM,7467
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 MLaaS/tfaas_client.py,sha256=zpZ201wwcQBW1XkzDakD9Kl_NRSESAUdbnN6k6Ey15A,14889
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