ChessAnalysisPipeline 0.0.3__py3-none-any.whl → 0.0.4__py3-none-any.whl

CHAP/common/utils/scanparsers.py

@@ -513,6 +513,19 @@ class RotationScanParser(ScanParser):
 class FMBRotationScanParser(RotationScanParser, FMBScanParser):
     def __init__(self, spec_file_name, scan_number):
         super().__init__(spec_file_name, scan_number)
+    def get_spec_scan_npts(self):
+        if self.spec_macro == 'flyscan':
+            if len(self.spec_args) == 2:
+                # Flat field (dark or bright)
+                return(int(self.spec_args[0])+1)
+            elif len(self.spec_args) == 5:
+                return(int(self.spec_args[3])+1)
+            else:
+                raise(RuntimeError(f'{self.scan_title}: cannot obtain number of points from '+
+                        f'{self.spec_macro} with arguments {self.spec_args}'))
+        else:
+            raise(RuntimeError(f'{self.scan_title}: cannot determine number of points for scans '+
+                    f'of type {self.spec_macro}'))
     def get_theta_vals(self):
         if self.spec_macro == 'flyscan':
             if len(self.spec_args) == 2:
@@ -525,7 +538,7 @@ class FMBRotationScanParser(RotationScanParser, FMBScanParser):
                 raise(RuntimeError(f'{self.scan_title}: cannot obtain theta values from '+
                         f'{self.spec_macro} with arguments {self.spec_args}'))
         else:
-            raise(RuntimeError(f'{self.scan_title}: cannot determine scan motors for scans '+
+            raise(RuntimeError(f'{self.scan_title}: cannot determine theta values for scans '+
                     f'of type {self.spec_macro}'))
     def get_horizontal_shift(self):
         return(0.0)
@@ -578,6 +591,11 @@ class SMBRotationScanParser(RotationScanParser, SMBScanParser):
     def __init__(self, spec_file_name, scan_number):
         super().__init__(spec_file_name, scan_number)
         self.par_file_pattern = f'id*-*tomo*-{self.scan_name}'
+    def get_spec_scan_npts(self):
+        if self.spec_macro == 'slew_ome' or self.spec_macro == 'rams4_slew_ome':
+            return(int(self.pars['nframes_real']))
+        else:
+            raise(RuntimeError(f'{self.scan_title}: cannot determine number of points for scans of type {self.spec_macro}'))
     def get_scan_type(self):
         try:
             return(self.pars['tomo_type'])

CHAP/edd/processor.py

@@ -8,10 +8,7 @@ Description: Module for Processors used only by EDD experiments
 '''
 
 # system modules
-import argparse
 import json
-import logging
-import sys
 
 # local modules
 from CHAP.processor import Processor

CHAP/pipeline.py

@@ -50,7 +50,7 @@ class Pipeline():
                 self.logger.info(f'Calling "write" on {item}')
                 data = item.write(data, **kwargs)
 
-        self.logger.info(f'Exectuted "exectute" in {time()-t0:.3f} seconds')
+        self.logger.info(f'Executed "execute" in {time()-t0:.3f} seconds')
 
 class PipelineObject():
     """

CHAP/tomo/__init__.py

@@ -0,0 +1,5 @@
+# from CHAP.tomo.reader import
+from CHAP.tomo.processor import TomoDataProcessor
+# from CHAP.tomo.writer import
+
+from CHAP.common import MapProcessor

CHAP/tomo/models.py

@@ -0,0 +1,125 @@
+# system modules
+
+# third party imports
+from pydantic import (
+        BaseModel,
+        StrictBool,
+        conint,
+        conlist,
+        confloat,
+        constr,
+)
+from typing import Literal, Optional
+
+
+class Detector(BaseModel):
+    """
+    Detector class to represent the detector used in the experiment.
+    
+    :ivar prefix: Prefix of the detector in the SPEC file.
+    :type prefix: str
+    :ivar rows: Number of pixel rows on the detector
+    :type rows: int
+    :ivar columns: Number of pixel columns on the detector
+    :type columns: int
+    :ivar pixel_size: Pixel size of the detector in mm
+    :type pixel_size: int or list[int]
+    :ivar lens_magnification: Lens magnification for the detector
+    :type lens_magnification: float, optional
+    """
+    prefix: constr(strip_whitespace=True, min_length=1)
+    rows: conint(gt=0)
+    columns: conint(gt=0)
+    pixel_size: conlist(item_type=confloat(gt=0, allow_inf_nan=False), min_items=1, max_items=2)
+    lens_magnification: confloat(gt=0, allow_inf_nan=False) = 1.0
+
+
+class TomoSetupConfig(BaseModel):
+    """
+    Class representing the configuration for the tomography reconstruction setup.
+
+    :ivar detectors: Detector used in the tomography experiment
+    :type detectors: Detector
+    """
+    detector: Detector.construct()
+    include_raw_data: Optional[StrictBool] = False
+
+
+class TomoReduceConfig(BaseModel):
+    """
+    Class representing the configuration for tomography image reductions.
+
+    :ivar tool_type: Type of tomography reconstruction tool; always set to "reduce_data"
+    :type tool_type: str, optional
+    :ivar detectors: Detector used in the tomography experiment
+    :type detectors: Detector
+    :ivar img_x_bounds: Detector image bounds in the x-direction
+    :type img_x_bounds: list[int], optional
+    """
+    tool_type: Literal['reduce_data'] = 'reduce_data'
+    detector: Detector = Detector.construct()
+    img_x_bounds: Optional[conlist(item_type=conint(ge=0), min_items=2, max_items=2)]
+
+
+class TomoFindCenterConfig(BaseModel):
+    """
+    Class representing the configuration for tomography find center axis.
+
+    :ivar tool_type: Type of tomography reconstruction tool; always set to "find_center"
+    :type tool_type: str, optional
+    :ivar center_stack_index: Stack index of tomography set to find center axis (offset 1)
+    :type center_stack_index: int, optional
+    :ivar lower_row: Lower row index for center finding
+    :type lower_row: int, optional
+    :ivar lower_center_offset: Center at lower row index
+    :type lower_center_offset: float, optional
+    :ivar upper_row: Upper row index for center finding
+    :type upper_row: int, optional
+    :ivar upper_center_offset: Center at upper row index
+    :type upper_center_offset: float, optional
+    """
+    tool_type: Literal['find_center'] = 'find_center'
+    center_stack_index: Optional[conint(ge=1)]
+    lower_row: Optional[conint(ge=-1)]
+    lower_center_offset: Optional[confloat(allow_inf_nan=False)]
+    upper_row: Optional[conint(ge=-1)]
+    upper_center_offset: Optional[confloat(allow_inf_nan=False)]
+
+
+class TomoReconstructConfig(BaseModel):
+    """
+    Class representing the configuration for tomography image reconstruction.
+
+    :ivar tool_type: Type of tomography reconstruction tool; always set to "reconstruct_data"
+    :type tool_type: str, optional
+    :ivar x_bounds: Reconstructed image bounds in the x-direction
+    :type x_bounds: list[int], optional
+    :ivar y_bounds: Reconstructed image bounds in the y-direction
+    :type y_bounds: list[int], optional
+    :ivar z_bounds: Reconstructed image bounds in the z-direction
+    :type z_bounds: list[int], optional
+    """
+    tool_type: Literal['reconstruct_data'] = 'reconstruct_data'
+    x_bounds: Optional[conlist(item_type=conint(ge=-1), min_items=2, max_items=2)]
+    y_bounds: Optional[conlist(item_type=conint(ge=-1), min_items=2, max_items=2)]
+    z_bounds: Optional[conlist(item_type=conint(ge=-1), min_items=2, max_items=2)]
+
+
+class TomoCombineConfig(BaseModel):
+    """
+    Class representing the configuration for combined tomography stacks.
+
+    :ivar tool_type: Type of tomography reconstruction tool; always set to "combine_data"
+    :type tool_type: str, optional
+    :ivar x_bounds: Reconstructed image bounds in the x-direction
+    :type x_bounds: list[int], optional
+    :ivar y_bounds: Reconstructed image bounds in the y-direction
+    :type y_bounds: list[int], optional
+    :ivar z_bounds: Reconstructed image bounds in the z-direction
+    :type z_bounds: list[int], optional
+    """
+    tool_type: Literal['combine_data'] = 'combine_data'
+    x_bounds: Optional[conlist(item_type=conint(ge=-1), min_items=2, max_items=2)]
+    y_bounds: Optional[conlist(item_type=conint(ge=-1), min_items=2, max_items=2)]
+    z_bounds: Optional[conlist(item_type=conint(ge=-1), min_items=2, max_items=2)]
+