Merge pull request #165 from dvm-shlee/main

Refactor and Ongoing Development in API Module

brkraw/api/analyzer/dataarray.py

@@ -18,9 +18,9 @@ def __init__(self, infoobj: 'ScanInfo', fileobj: Union[BufferedReader, ZipExtFil
     def _parse_info(self, infoobj: 'ScanInfo'):
         if not hasattr(infoobj, 'dataarray'):
             raise AttributeError
-        self.slope = infoobj.dataarray['2dseq_slope']
-        self.offset = infoobj.dataarray['2dseq_offset']
-        self.dtype = infoobj.dataarray['2dseq_dtype']
+        self.slope = infoobj.dataarray['slope']
+        self.offset = infoobj.dataarray['offset']
+        self.dtype = infoobj.dataarray['dtype']
         self.shape = infoobj.image['shape'][:]
         self.shape_desc = infoobj.image['dim_desc'][:]
         if infoobj.frame_group and infoobj.frame_group['type']:

brkraw/api/analyzer/scaninfo.py

@@ -25,6 +25,7 @@ def __init__(self,
         self._set_pars(pvobj, reco_id)
         if not debug:
             self.info_protocol = helper.Protocol(self).get_info()
+            self.info_fid = helper.FID(self).get_info()
             if self.visu_pars:
                 self._parse_info()
 

brkraw/api/brkobj/scan.py

@@ -31,7 +31,7 @@ def __init__(self, pvscan: 'PvScan', reco_id: Optional[int] = None,
     def set_info(self):
         self.info = self.get_info(self.reco_id)
 
-    def get_info(self, reco_id:int, get_analyzer:bool = False):
+    def get_info(self, reco_id:Optional[int] = None, get_analyzer:bool = False):
         infoobj = ScanInfo()
         pvscan = self.retrieve_pvscan()
         analysed = ScanInfoAnalyzer(pvscan, reco_id, self.is_debug)

brkraw/api/helper/__init__.py

@@ -5,6 +5,7 @@
 from .slicepack import SlicePack
 from .cycle import Cycle
 from .orientation import Orientation, to_matvec, from_matvec, rotate_affine
+from .fid import FID
 
-__all__ = [Protocol, FrameGroup, DataArray, Image, SlicePack, Cycle, Orientation, 
+__all__ = [Protocol, FID, FrameGroup, DataArray, Image, SlicePack, Cycle, Orientation, 
            to_matvec, from_matvec, rotate_affine]

brkraw/api/helper/base.py

@@ -1,6 +1,17 @@
 import warnings
 from functools import partial
 
+WORDTYPE = \
+    dict(_32BIT_SGN_INT     = 'i',
+         _16BIT_SGN_INT     = 'h',
+         _8BIT_UNSGN_INT    = 'B',
+         _32BIT_FLOAT       = 'f')
+
+BYTEORDER = \
+    dict(littleEndian       = '<',
+         bigEndian          = '>')
+
+
 def is_all_element_same(listobj):
     if listobj is None:
         return True

brkraw/api/helper/dataarray.py

@@ -1,22 +1,11 @@
 from __future__ import annotations
 import numpy as np
 from typing import TYPE_CHECKING
-from .base import BaseHelper, is_all_element_same
+from .base import BaseHelper, is_all_element_same, BYTEORDER, WORDTYPE
 if TYPE_CHECKING:
     from ..analyzer import ScanInfoAnalyzer
 
 
-WORDTYPE = \
-    dict(_32BIT_SGN_INT     = 'i',
-         _16BIT_SGN_INT     = 'h',
-         _8BIT_UNSGN_INT    = 'B',
-         _32BIT_FLOAT       = 'f')
-
-BYTEORDER = \
-    dict(littleEndian       = '<',
-         bigEndian          = '>')
-
-
 class DataArray(BaseHelper):
     """requires visu_pars and aqcp to pars parameter related to the dtype of binary files
 
@@ -29,17 +18,8 @@ class DataArray(BaseHelper):
     """
     def __init__(self, analobj: 'ScanInfoAnalyzer'):
         super().__init__()
-        acqp = analobj.acqp
         visu_pars = analobj.visu_pars
 
-        if acqp:
-            fid_word_type = f'_{"".join(acqp["ACQ_word_size"].split("_"))}_SGN_INT'
-            fid_byte_order = f'{acqp["BYTORDA"]}Endian'
-            self.fid_dtype = np.dtype(f'{BYTEORDER[fid_byte_order]}{WORDTYPE[fid_word_type]}')
-        else:
-            self.fid_dtype = None
-            self._warn("Failed to fetch 'fid_dtype' information because the 'acqp' file is missing from 'analobj'.")
-
         byte_order = visu_pars["VisuCoreByteOrder"]
         word_type = visu_pars["VisuCoreWordType"]
         self.data_dtype = np.dtype(f'{BYTEORDER[byte_order]}{WORDTYPE[word_type]}')
@@ -53,13 +33,13 @@ def __init__(self, analobj: 'ScanInfoAnalyzer'):
 
         if isinstance(self.data_slope, list) or isinstance(self.data_offset, list):
             self._warn("Data slope and data offset values are unusual. "
-                       "They are expected to be either a list containing the same elements or a single float value.")
+                    "They are expected to be either a list containing the same elements or a single float value.")
+
 
     def get_info(self):
         return {
-            'fid_dtype': self.fid_dtype,
-            '2dseq_dtype': self.data_dtype,
-            '2dseq_slope': self.data_slope,
-            '2dseq_offset': self.data_offset,
+            'dtype': self.data_dtype,
+            'slope': self.data_slope,
+            'offset': self.data_offset,
             'warns': self.warns
         }

brkraw/api/helper/fid.py

@@ -0,0 +1,36 @@
+from __future__ import annotations
+import numpy as np
+from typing import TYPE_CHECKING
+from .base import BaseHelper, is_all_element_same, BYTEORDER, WORDTYPE
+if TYPE_CHECKING:
+    from ..analyzer import ScanInfoAnalyzer
+
+
+class FID(BaseHelper):
+    """requires visu_pars and aqcp to pars parameter related to the dtype of binary files
+
+    Dependencies:
+        acqp
+        visu_pars
+
+    Args:
+        BaseHelper (_type_): _description_
+    """
+    def __init__(self, analobj: 'ScanInfoAnalyzer'):
+        super().__init__()
+        acqp = analobj.acqp
+
+        if acqp:
+            word_type = f'_{"".join(acqp["ACQ_word_size"].split("_"))}_SGN_INT'
+            byte_order = f'{acqp["BYTORDA"]}Endian'
+            self.dtype = np.dtype(f'{BYTEORDER[byte_order]}{WORDTYPE[word_type]}')
+        else:
+            self.fid_dtype = None
+            self._warn("Failed to fetch 'fid_dtype' information because the 'acqp' file is missing from 'analobj'.")
+
+
+    def get_info(self):
+        return {
+            'dtype': self.dtype,
+            'warns': self.warns
+        }

brkraw/api/helper/orientation.py

@@ -245,6 +245,7 @@ def _calc_eulerangle(matrix):
     def _get_gradient_encoding_dir(cls, visu_pars):
         if visu_pars["VisuVersion"] != 1:
             return visu_pars["VisuAcqGradEncoding"]
+        # routine for PV version < 6
         phase_enc = visu_pars["VisuAcqImagePhaseEncDir"]
         phase_enc = phase_enc[0] if is_all_element_same(phase_enc) else phase_enc
         return (

pyproject.toml

@@ -16,7 +16,8 @@ dependencies = [
     'pillow>=7.1.1',
     'tqdm>=4.45.0',
     'openpyxl>=3.0.3',
-    'xlrd>=1.0.0'
+    'xlrd>=1.0.0',
+    'toml>=0.10.2'
 ]
 description = "Bruker PvDataset Loader"
 license = {text = "GNLv3"}