[WIP] rearranging BIDSMRI2NIDM command

nidm/experiment/__init__.py

@@ -8,3 +8,5 @@
 from .MRObject import MRObject
 from .DemographicsObject import DemographicsObject
 from .AssessmentObject import AssessmentObject
+from .bids_base import BidsNidm
+from .bidsmri import BidsMriNidm

nidm/experiment/bids_base.py

@@ -0,0 +1,157 @@
+import os, glob, json, csv, pdb
+import logging
+import pandas as pd
+from nidm.core import BIDS_Constants, Constants
+from nidm.experiment.Utils import map_variables_to_terms
+from nidm.experiment import (Project, Session, MRAcquisition, AcquisitionObject, DemographicsObject,
+                             AssessmentAcquisition, AssessmentObject, MRObject)
+from bids.grabbids import BIDSLayout
+
+
+class BidsNidm(object):
+    def __init__(self, directory, json_map=None, github=None, key=None, owl=None):
+        self.directory = directory
+        self.json_map = json_map
+        self.github = github
+        self.key = key
+        self.owl = owl
+        self.project = self._create_project()
+        # get BIDS layout
+        self.bids_layout = BIDSLayout(directory)
+
+        self._create_session_participants()
+
+
+    @property
+    def directory(self):
+        if self._directory:
+            return self._directory
+
+    @directory.setter
+    def directory(self, value):
+        if os.path.isdir(value):
+            self._directory = value
+            try:
+                with open(os.path.join(self._directory, 'dataset_description.json')) as data_file:
+                    self.dataset = json.load(data_file)
+            except OSError:
+                raise Exception("Cannot find dataset_description.json file which is required in the BIDS spec")
+
+        else:
+            # TODO: ask DK
+            raise Exception("Error: BIDS directory %s does not exist!" % os.path.join(value))
+            #logging.critical("Error: BIDS directory %s does not exist!" % os.path.join(value))
+            #exit("-1")
+
+
+    def _create_project(self):
+        #create project / nidm-exp doc
+        project = Project()
+
+        #add various attributes if they exist in BIDS dataset
+        for key in self.dataset:
+            #if key from dataset_description file is mapped to term in BIDS_Constants.py then add to NIDM object
+            if key in BIDS_Constants.dataset_description:
+                if type(self.dataset[key]) is list:
+                    project.add_attributes({BIDS_Constants.dataset_description[key]: "".join(self.dataset[key])})
+                else:
+                    project.add_attributes({BIDS_Constants.dataset_description[key]: self.dataset[key]})
+            #add absolute location of BIDS directory on disk for later finding of files which are stored relatively in NIDM document
+            project.add_attributes({Constants.PROV['Location']: self.directory})
+        return project
+
+
+    def _create_session_participants(self):
+        """ Create empty dictionary for sessions where key is subject id
+        and used later to link scans to same session as demographics
+        """
+        self.session = {}
+        self.participant = {}
+
+        #Parse participants.tsv file in BIDS directory and create study and acquisition objects
+        if os.path.isfile(os.path.join(self.directory, 'participants.tsv')):
+            with open(os.path.join(self.directory, 'participants.tsv')) as csvfile:
+                participants_data = csv.DictReader(csvfile, delimiter='\t')
+
+                # logic to map variables to terms.
+
+                # first iterate over variables in dataframe and check which ones are already mapped as BIDS constants
+                # and which are not.  For those that are not
+                # we want to use the variable-term mapping functions to help the user do the mapping
+                # iterate over columns
+                mapping_list = []
+                column_to_terms = {}
+                for field in participants_data.fieldnames:
+                    #column is not in BIDS_Constants
+                    if not (field in BIDS_Constants.participants):
+                        #add column to list for column_to_terms mapping
+                        mapping_list.append(field)
+
+                #do variable-term mappings
+                if self.json_map or self.key or self.github:
+                     # if user didn't supply a json mapping file but we're doing some variable-term mapping
+                     # create an empty one for column_to_terms to use
+                     if self.json_map is None:
+                        #defaults to participants.json because here we're mapping the participants.tsv file variables to terms
+                        self.json_map = os.path.isfile(os.path.join(self.directory, 'participants.json'))
+
+                     #maps variables in CSV file to terms
+                     temp = pd.DataFrame(columns=mapping_list)
+                     column_to_terms.update(map_variables_to_terms(directory=self.directory, df=temp, apikey=self.key,
+                                                                   output_file=self.json_map, json_file=self.json_map,
+                                                                   github=self.github, owl_file=self.owl))
+
+
+
+                for row in participants_data:
+                    #create session object for subject to be used for participant metadata and image data
+                    #parse subject id from "sub-XXXX" string
+                    temp = row['participant_id'].split("-")
+                    #for ambiguity in BIDS datasets.  Sometimes participant_id is sub-XXXX and othertimes it's just XXXX
+                    if len(temp) > 1:
+                        subjid = temp[1]
+                    else:
+                        subjid = temp[0]
+                    logging.info(subjid)
+                    self.session[subjid] = Session(self.project)
+
+                    #add acquisition object
+                    acq = AssessmentAcquisition(session=self.session[subjid])
+
+                    acq_entity = AssessmentObject(acquisition=acq)
+                    self.participant[subjid] = {}
+                    self.participant[subjid]['person'] = acq.add_person(attributes=({Constants.NIDM_SUBJECTID:row['participant_id']}))
+
+
+                    #add qualified association of participant with acquisition activity
+                    acq.add_qualified_association(person=self.participant[subjid]['person'], role=Constants.NIDM_PARTICIPANT)
+
+
+                    # TODO: check with DK where acq_entity is used
+                    for key, value in row.items():
+                        # for variables in participants.tsv file who have term mappings in BIDS_Constants.py use those,
+                        # add to json_map so we don't have to map these if user
+                        # supplied arguments to map variables
+                        if key in BIDS_Constants.participants:
+                            #if this was the participant_id, we already handled it above creating agent / qualified association
+                            if BIDS_Constants.participants[key] != Constants.NIDM_SUBJECTID:
+                                acq_entity.add_attributes({BIDS_Constants.participants[key]:value})
+
+
+                        #else if user added -mapvars flag to command line then we'll use the variable-> term mapping procedures
+                        # to help user map variables to terms (also used in CSV2NIDM.py)
+                        elif key in column_to_terms:
+                            acq_entity.add_attributes({QualifiedName(provNamespace(Core.safe_string(None,string=str(key)), column_to_terms[key]["url"]), ""):value})
+                        else:
+                            acq_entity.add_attributes({Constants.BIDS[key.replace(" ", "_")]:value})
+
+
+    def _getRelPathToBIDS(self, filepath):
+        """This function returns a relative file link that is relative to the BIDS root directory.
+        :param filename: absolute path + file
+        :param bids_root: absolute path to BIDS directory
+        :return: relative path to file, relative to BIDS root
+        """
+        path, file = os.path.split(filepath)
+        relpath = path.replace(self.directory, "")
+        return os.path.join(relpath, file)