FIX BlockMeta repeat #20 ?

brukeropusreader/block_data.py

@@ -19,17 +19,30 @@ class UnknownBlockType(Exception):
     },
 )
 
-BLOCK_7 = {4: "ScSm", 8: "IgSm", 12: "PhSm"}
+# other sample spectral data (single channel, interferogram, power spectrum, ...)
+BLOCK_7 = {4: "ScSm", 8: "IgSm", 12: "PhSm", 56: "PwSm", 132: "ScSm_(1)", 136: "IgSm_(1)"}
 
-BLOCK_11 = {4: "ScRf", 8: "IgRf"}
+# other reference spectral data (single channel, interferogram, power spectrum, ...)
+BLOCK_11 = {4: "ScRf", 8: "IgRf", 56: "PwRf", 132: "ScRf_(1)", 136: "IgRf_(1)"}
 
+# parameters of other sample spectral data
 BLOCK_23 = {
     4: "ScSm Data Parameter",
     8: "IgSm Data Parameter",
     12: "PhSm Data Parameter",
+    56: "PwSm Data Parameter",
+    132: "ScSm_(1) Data Parameter",
+    136: "IgSm_(1) Data Parameter",
 }
 
-BLOCK_27 = {4: "ScRf Data Parameter", 8: "IgRf Data Parameter"}
+# parameters of other reference spectral data
+BLOCK_27 = {
+    4: "ScRf Data Parameter",
+    8: "IgRf Data Parameter",
+    56: "PwRf Data Parameter",
+    132: "ScRf_(1) Data Parameter",
+    136: "IgRf_(1) Data Parameter",
+}
 
 DIFFERENT_BLOCKS = {
     31: "AB Data Parameter",
@@ -51,12 +64,14 @@ def __init__(
         data_type: int,
         channel_type: int,
         text_type: int,
+        additional_type: int,
         chunk_size: int,
         offset: int,
     ):
         self.data_type = data_type
         self.channel_type = channel_type
         self.text_type = text_type
+        self.additional_type = additional_type
         self.chunk_size = chunk_size
         self.offset = offset
 

brukeropusreader/block_parser.py

@@ -6,13 +6,17 @@
     NULL_BYTE,
     ENCODING_LATIN,
     ENCODING_UTF,
-    NULL_STR)
+    NULL_STR,
+)
 from brukeropusreader.opus_reader import read_chunk
 from struct import unpack, error
 import numpy as np
 
 
 def parse_param(data: bytes, block_meta):
+    """parse data blocks of parameters
+
+    BLOCK_23, BLOCK_27"""
     cursor = 0
     chunk = read_chunk(data, block_meta)
     params = {}

brukeropusreader/opus_parser.py

@@ -11,6 +11,7 @@
     read_data_type,
     read_channel_type,
     read_text_type,
+    read_additional_type,
     read_chunk_size,
     read_offset,
 )
@@ -25,6 +26,15 @@ def read_file(file_path: str) -> OpusData:
 
 
 def parse_meta(data: bytes) -> List[BlockMeta]:
+    """Parse the header of the opus file.
+
+    Returns a list of metadata (BlockMeta) for each block to be read,
+
+    :parameter:
+        data: bytes content of the opus file
+    :returns:
+        parse_meta: list of BlockMeta
+    """
     header = data[:HEADER_LEN]
     spectra_meta = []
     cursor = FIRST_CURSOR_POSITION
@@ -35,14 +45,14 @@ def parse_meta(data: bytes) -> List[BlockMeta]:
         data_type = read_data_type(header, cursor)
         channel_type = read_channel_type(header, cursor)
         text_type = read_text_type(header, cursor)
+        additional_type = read_additional_type(header, cursor)
         chunk_size = read_chunk_size(header, cursor)
         offset = read_offset(header, cursor)
 
         if offset <= 0:
             break
 
-        block_meta = BlockMeta(data_type, channel_type,
-                               text_type, chunk_size, offset)
+        block_meta = BlockMeta(data_type, channel_type, text_type, additional_type, chunk_size, offset)
 
         spectra_meta.append(block_meta)
 
@@ -54,12 +64,21 @@ def parse_meta(data: bytes) -> List[BlockMeta]:
 
 
 def parse_data(data: bytes, blocks_meta: List[BlockMeta]) -> OpusData:
+    """parse the data of the opus file using the file header's informations
+    parame"""
     opus_data = OpusData()
     for block_meta in blocks_meta:
         try:
             name, parser = block_meta.get_name_and_parser()
         except UnknownBlockType:
             continue
         parsed_data = parser(data, block_meta)
+        # in some instances, multiple entries - in particular 'AB' are
+        # present. they are added with a key ending by '_(1)', '_(2)', etc...
+        if name in opus_data.keys():
+            i = 1
+            while name + '_(' + str(i) + ')' in opus_data.keys():
+                i += 1
+            name = name + '_(' + str(i) + ')'
         opus_data[name] = parsed_data
     return opus_data

brukeropusreader/opus_reader.py

@@ -21,6 +21,12 @@ def read_text_type(header: bytes, cursor: int) -> int:
     return unpack(UNSIGNED_CHAR, header[p1:p2])[0]
 
 
+def read_additional_type(header: bytes, cursor: int) -> int:
+    p1 = cursor + 3
+    p2 = cursor + 4
+    return unpack(UNSIGNED_CHAR, header[p1:p2])[0]
+
+
 def read_chunk_size(header: bytes, cursor: int) -> int:
     p1 = cursor + 4
     p2 = cursor + 8

recipe/meta.yaml.bak

@@ -0,0 +1,52 @@
+{% set name = "brukeropusreader" %}
+{% set version = environ['VERSION'] %}
+
+package:
+  name: "{{ name|lower }}"
+  version: "{{ version }}"
+
+source:
+  path: ../
+
+build:
+  script_env:
+    - VERSION
+    - CONDA_BLD_PATH
+  string: {{ environ['DEVSTRING'] }}
+  noarch: python
+  script: "{{ PYTHON }} -m pip install . -vv"
+
+requirements:
+  build:
+    - python
+  host:
+    - python
+    - numpy
+    - pip
+    - scipy
+  run:
+    - python
+    - numpy
+    - scipy
+  test:
+    - python             {{ python }}
+    - pytest
+
+test:
+  script_env:
+    - VERSION
+    - CONDA_BLD_PATH
+  imports:
+    - brukeropusreader
+
+about:
+  home: "https://github.com/spectrochempy/brukeropusreader"
+  license: GPLv3
+  license_family: GPL3
+  summary: "Bruker OPUS File Reader"
+  doc_url: "https://github.com/spectrochempy/brukeropusreader"
+  dev_url: "https://github.com/spectrochempy/brukeropusreader"
+
+extra:
+  recipe-maintainers:
+    - fernandezc