ChessAnalysisPipeline 0.0.5__py3-none-any.whl → 0.0.6__py3-none-any.whl

CHAP/tomo/models.py

@@ -1,21 +1,24 @@
-# system modules
+"""Tomography Pydantic model classes"""
 
-# third party imports
+# Third party imports
+from typing import (
+    Literal,
+    Optional,
+)
 from pydantic import (
-        BaseModel,
-        StrictBool,
-        conint,
-        conlist,
-        confloat,
-        constr,
+    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
@@ -25,21 +28,27 @@ class Detector(BaseModel):
     :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
+    :type lens_magnification: float, optional [1.0]
     """
     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)
+    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.
+    Class representing the configuration for the tomography
+    reconstruction setup.
 
     :ivar detectors: Detector used in the tomography experiment
     :type detectors: Detector
+    :ivar include_raw_data: Flag to designate whether raw data will be
+        included (True) or not (False)
+    :type include_raw_data: bool, optional [False]
     """
     detector: Detector.construct()
     include_raw_data: Optional[StrictBool] = False
@@ -47,9 +56,11 @@ class TomoSetupConfig(BaseModel):
 
 class TomoReduceConfig(BaseModel):
     """
-    Class representing the configuration for tomography image reductions.
+    Class representing the configuration for tomography image
+    reductions.
 
-    :ivar tool_type: Type of tomography reconstruction tool; always set to "reduce_data"
+    :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
@@ -58,16 +69,19 @@ class TomoReduceConfig(BaseModel):
     """
     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)]
+    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"
+    :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)
+    :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
@@ -88,9 +102,11 @@ class TomoFindCenterConfig(BaseModel):
 
 class TomoReconstructConfig(BaseModel):
     """
-    Class representing the configuration for tomography image reconstruction.
+    Class representing the configuration for tomography image
+    reconstruction.
 
-    :ivar tool_type: Type of tomography reconstruction tool; always set to "reconstruct_data"
+    :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
@@ -100,26 +116,32 @@ class TomoReconstructConfig(BaseModel):
     :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)]
+    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"
+    :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
+    :ivar x_bounds: Combined image bounds in the x-direction
     :type x_bounds: list[int], optional
-    :ivar y_bounds: Reconstructed image bounds in the y-direction
+    :ivar y_bounds: Combined image bounds in the y-direction
     :type y_bounds: list[int], optional
-    :ivar z_bounds: Reconstructed image bounds in the z-direction
+    :ivar z_bounds: Combined 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)]
-
+    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)]