Merge branch 'nb_fixes' into 'dev'

Minor fixes

See merge request CyclotronResearchCentre/Public/bidstools/bidsme/bidsme!10

CHANGELOG.md

@@ -3,6 +3,14 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 
+### Fixed
+  - jsonNIFTI: fixed retrieval of ParticipantID, based on `dcm2niix` entry `PatientID`
+  - BaseModule: `series_no`/`series_id` becomes prperties with type check (int/str resp.)
+
+### Added
+  - Log entry while loading tables
+  - NIFTI: added support for compressed files
+
 ## [1.6.4] - 2024-04-11
 
 ### Fixed

bidsme/Modules/MRI/NIFTI.py

@@ -52,7 +52,7 @@ class NIFTI(MRI):
                        "PatientId",
                        "SessionId"}
 
-    _file_extentions = [".nii", ".hdr"]
+    _file_extentions = [".nii", ".nii.gz", ".hdr"]
 
     def __init__(self, rec_path=""):
         super().__init__()

bidsme/Modules/MRI/jsonNIFTI.py

@@ -170,7 +170,7 @@ def copyRawFile(self, destination: str) -> str:
         return os.path.join(destination, self.currentFile(True))
 
     def _getSubId(self) -> str:
-        return ""
+        return self.getField("PatientID", "")
 
     def _getSesId(self) -> str:
         return ""

bidsme/Modules/PET/NIFTI.py

@@ -46,7 +46,7 @@ class NIFTI(PET):
     __slots__ = ["_NIFTI_CACHE", "_FILE_CACHE",
                  "_nii_type", "_endiannes"
                  ]
-    _file_extentions = [".nii", ".hdr"]
+    _file_extentions = [".nii", ".nii.gz", ".hdr"]
 
     __specialFields = {"AcquisitionTime",
                        "SeriesNumber",

bidsme/Modules/PET/jsonNIFTI.py

@@ -162,7 +162,16 @@ def copyRawFile(self, destination: str) -> str:
         return os.path.join(destination, self.currentFile(True))
 
     def _getSubId(self) -> str:
-        return ""
+        tags = ["patient_id",  # ecat header dump
+                "PatientID"  # dcm2niix
+                ]
+        res = ""
+        for t in tags:
+            res = self.getField(t, "")
+            if res:
+                break
+
+        return res
 
     def _getSesId(self) -> str:
         return ""

bidsme/Modules/_nifti_common.py

@@ -23,11 +23,33 @@
 
 import logging
 import struct
+import gzip
 
 
 logger = logging.getLogger(__name__)
 
 
+def _nii_open(path: str, mode="rb"):
+    """
+    Returns open file stream with open or gzip.open
+
+    Parameters:
+    -----------
+    path: str
+        Path to file to open
+    mode: str
+        Mode in wich open
+
+    Returns:
+    --------
+    (decompressed) opened stream
+    """
+    if path.endswith('.gz'):
+        return gzip.open(path, mode)
+    else:
+        return open(path, mode)
+
+
 def isValidNIFTI(file: str) -> bool:
     """
     Returns True if given file is valid, i.e.
@@ -39,8 +61,10 @@ def isValidNIFTI(file: str) -> bool:
     file: str
         path to file (must exist)
     """
-    with open(file, 'rb') as niifile:
+
+    with _nii_open(file, 'rb') as niifile:
         d = niifile.read(4)
+
         if len(d) != 4:
             logger.debug('File too short')
             return False
@@ -79,7 +103,7 @@ def getEndType(path: str) -> tuple:
     (str, str):
         tuple of endianess symbol and nifti type
     """
-    with open(path, "rb") as niifile:
+    with _nii_open(path, "rb") as niifile:
         header_size = struct.unpack("<i", niifile.read(4))[0]
         if header_size in (348, 540):
             endian = "<"
@@ -138,7 +162,7 @@ def parceNIFTIheader_1(path: str, endian: str) -> dict:
         parced header
     """
     res = dict()
-    with open(path, "rb") as niifile:
+    with _nii_open(path, "rb") as niifile:
         header = niifile.read(348)
 
     diminfo = struct.unpack("c", header[39:40])[0]
@@ -199,7 +223,7 @@ def parceNIFTIheader_2(path: str, endian: str) -> dict:
         parced header
     """
     res = dict()
-    with open(path, "rb") as niifile:
+    with _nii_open(path, "rb") as niifile:
         header = niifile.read(540)
 
     res["datatype"] = struct.unpack(endian + "h", header[12:14])[0]

bidsme/Modules/base.py

@@ -68,8 +68,8 @@ class baseModule(abstract):
                  "files",
                  "_recPath",
                  # series identifier
-                 "series_id",
-                 "series_no",
+                 "_series_id",
+                 "_series_no",
                  # json meta variables
                  "metaAuxiliary",
                  "metaFields_req",
@@ -132,8 +132,8 @@ def __init__(self):
         self.files = list()
         self._recPath = ""
         self.index = -1
-        self.series_id = None
-        self.series_no = None
+        self._series_id = None
+        self._series_no = None
         self.attributes = dict()
         self.custom = dict()
         self.labels = OrderedDict()
@@ -801,9 +801,31 @@ def resetAcqTime(self):
         """
         self._acqTime = None
 
+    @property
+    def series_no(self):
+        return self._series_no
+
+    @series_no.setter
+    def series_no(self, val):
+        if not isinstance(val, int):
+            raise ValueError("{}: series_no must be an int, {} recieved"
+                             .format(self.currentFile(), type(val)))
+        self._series_no = val
+
     def recNo(self):
         return self.series_no
 
+    @property
+    def series_id(self):
+        return self._series_id
+
+    @series_id.setter
+    def series_id(self, val):
+        if not isinstance(val, str):
+            raise ValueError("{}: series_id must be a string, {} recieved"
+                             .format(self.currentFile(), type(val)))
+        self._series_id = val
+
     def recId(self):
         return self.series_id
 

bidsme/bidsMeta/BidsTable.py

@@ -131,11 +131,15 @@ def __init__(self, table: str,
                 else:
                     for c in mismatch:
                         self.df[c] = None
+            logger.info("Loaded {} table with {} entries"
+                        .format(self._name, len(self.df)))
         else:
             columns = self._definitions.keys()
             if index and index not in columns:
                 columns = [index] + list(columns)
             self.df = pandas.DataFrame(columns=columns)
+            logger.info("Created empty {} table"
+                        .format(self._name))
 
     def getTablePath(self) -> str:
         """