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Pare down giant comment blocks that largely do what Git already does #363
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,33 +1,5 @@ | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| # nidm_query.py | ||
| # License: GPL | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| # Date: 8-1-18 Coded by: David Keator ([email protected]) | ||
| # Filename: nidm_query.py | ||
| # | ||
| # Program description: This program provides query functionality for NIDM-Experiment files | ||
| # | ||
| # | ||
| # ***************************************************************************** | ||
| # Development environment: Python - PyCharm IDE | ||
| # | ||
| # ***************************************************************************** | ||
| # System requirements: Python 3.X | ||
| # Libraries: os, sys, rdflib, pandas, argparse, logging | ||
| # ***************************************************************************** | ||
| # Start date: 8-1-18 | ||
| # Update history: | ||
| # DATE MODIFICATION Who | ||
| # | ||
| # | ||
| # ***************************************************************************** | ||
| # Programmer comments: | ||
| # | ||
| # | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| """This program provides query functionality for NIDM-Experiment files""" | ||
|
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| import functools | ||
| import hashlib | ||
| import json | ||
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,30 +1,8 @@ | ||
| # !/usr/bin/env python | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| # bidsmri2nidm.py | ||
| # License: Apache License, Version 2.0 | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| # Date: 10-2-17 Coded by: David Keator ([email protected]) | ||
| # Filename: bidsmri2nidm.py | ||
| # | ||
| # Program description: This program will convert a BIDS MRI dataset to a NIDM-Experiment | ||
| # RDF document. It will parse phenotype information and simply store variables/values | ||
| # and link to the associated json data dictionary file. | ||
| # | ||
| # ***************************************************************************** | ||
| # Development environment: Python - PyCharm IDE | ||
| # | ||
| # ***************************************************************************** | ||
| # System requirements: Python 3.X | ||
| # Libraries: pybids, numpy, matplotlib, pandas, scipy, math, dateutil, datetime,argparse, | ||
| # os,sys,getopt,csv | ||
| # ***************************************************************************** | ||
| # Programmer comments: | ||
| # | ||
| # | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| """ | ||
| This program will convert a BIDS MRI dataset to a NIDM-Experiment RDF document. | ||
| It will parse phenotype information and simply store variables/values and link | ||
| to the associated json data dictionary file. | ||
| """ | ||
|
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| from argparse import ArgumentParser, RawTextHelpFormatter | ||
| import csv | ||
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,33 +1,10 @@ | ||
| #!/usr/bin/env python | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| # csv2nidm.py | ||
| # License:Apache License, Version 2.0 | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| # Date: 01-19-18 Coded by: David Keator ([email protected]) | ||
| # Filename: csv2nidm.py | ||
| # | ||
| # Program description: This program will load in a CSV file and iterate over the header | ||
| # variable names performing an elastic search of https://scicrunch.org/ for NIDM-ReproNim | ||
| # tagged terms that fuzzy match the variable names. The user will then interactively pick | ||
| # a term to associate with the variable name. The resulting annotated CSV data will | ||
| # then be written to a NIDM data file. | ||
| # | ||
| # ***************************************************************************** | ||
| # Development environment: Python - PyCharm IDE | ||
| # | ||
| # ***************************************************************************** | ||
| # System requirements: Python 3.X | ||
| # Libraries: pybids, numpy, matplotlib, pandas, scipy, math, dateutil, datetime,argparse, | ||
| # os,sys,getopt,csv | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| # Programmer comments: | ||
| # | ||
| # | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| """ | ||
| This program will load in a CSV file and iterate over the header variable names | ||
| performing an elastic search of https://scicrunch.org/ for NIDM-ReproNim tagged | ||
| terms that fuzzy match the variable names. The user will then interactively | ||
| pick a term to associate with the variable name. The resulting annotated CSV | ||
| data will then be written to a NIDM data file. | ||
| """ | ||
|
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| from argparse import ArgumentParser | ||
| from io import StringIO | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,38 +1,11 @@ | ||
| #!/usr/bin/env python | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| # NIDM2BIDSMRI.py | ||
| # License: Apache License, Version 2.0 | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| # Date: 10-2-17 Coded by: David Keator ([email protected]) | ||
| # Filename: NIDM2BIDSMRI.py | ||
| # | ||
| # Program description: This program will convert a NIDM-Experiment RDF document | ||
| # to a BIDS dataset. The program will query the NIDM-Experiment document for subjects, | ||
| # MRI scans, and associated assessments saving the MRI data to disk in an organization | ||
| # according to the BIDS specification, the demographics metadata to a participants.tsv | ||
| # file, the project-level metadata to a dataset_description.json file, and the | ||
| # assessments to *.tsv/*.json file pairs in a phenotypes directory. | ||
| # ***************************************************************************** | ||
| # Development environment: Python - PyCharm IDE | ||
| # | ||
| # ***************************************************************************** | ||
| # System requirements: Python 3.X | ||
| # Libraries: pybids, numpy, matplotlib, pandas, scipy, math, dateutil, datetime,argparse, | ||
| # os,sys,getopt,csv | ||
| # ***************************************************************************** | ||
| # Start date: 10-2-17 | ||
| # Update history: | ||
| # DATE MODIFICATION Who | ||
| # | ||
| # | ||
| # ***************************************************************************** | ||
| # Programmer comments: | ||
| # | ||
| # | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| """ | ||
| This program will convert a NIDM-Experiment RDF document to a BIDS dataset. | ||
| The program will query the NIDM-Experiment document for subjects, MRI scans, | ||
| and associated assessments saving the MRI data to disk in an organization | ||
| according to the BIDS specification, the demographics metadata to a | ||
| participants.tsv file, the project-level metadata to a dataset_description.json | ||
| file, and the assessments to *.tsv/*.json file pairs in a phenotypes directory. | ||
| """ | ||
|
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||
| from argparse import ArgumentParser | ||
| from io import StringIO | ||
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,34 +1,4 @@ | ||
| #!/usr/bin/env python | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| # nidm_utils.py | ||
| # License: Apache License, Version 2.0 | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| # Date: 11-28-18 Coded by: David Keator ([email protected]) | ||
| # Filename: nidm_utils.py | ||
| # | ||
| # Program description: Tools for working with NIDM-Experiment files | ||
| # | ||
| # ***************************************************************************** | ||
| # Development environment: Python - PyCharm IDE | ||
| # | ||
| # ***************************************************************************** | ||
| # System requirements: Python 3.X | ||
| # Libraries: pybids, numpy, matplotlib, pandas, scipy, math, dateutil, datetime,argparse, | ||
| # os,sys,getopt,csv | ||
| # ***************************************************************************** | ||
| # Start date: 11-28-18 | ||
| # Update history: | ||
| # DATE MODIFICATION Who | ||
| # | ||
| # | ||
| # ***************************************************************************** | ||
| # Programmer comments: | ||
| # | ||
| # | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| """Tools for working with NIDM-Experiment files""" | ||
|
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| import click | ||
| from nidm.experiment.Query import GetMergedGraph | ||
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,34 +1,4 @@ | ||
| #!/usr/bin/env python | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| # nidm_utils.py | ||
| # License: Apache License, Version 2.0 | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| # Date: 11-28-18 Coded by: David Keator ([email protected]) | ||
| # Filename: nidm_utils.py | ||
| # | ||
| # Program description: Tools for working with NIDM-Experiment files | ||
| # | ||
| # ***************************************************************************** | ||
| # Development environment: Python - PyCharm IDE | ||
| # | ||
| # ***************************************************************************** | ||
| # System requirements: Python 3.X | ||
| # Libraries: pybids, numpy, matplotlib, pandas, scipy, math, dateutil, datetime,argparse, | ||
| # os,sys,getopt,csv | ||
| # ***************************************************************************** | ||
| # Start date: 11-28-18 | ||
| # Update history: | ||
| # DATE MODIFICATION Who | ||
| # | ||
| # | ||
| # ***************************************************************************** | ||
| # Programmer comments: | ||
| # | ||
| # | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| """ Tools for working with NIDM-Experiment files """ | ||
|
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| from os.path import basename, join, splitext | ||
| import click | ||
|
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||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,35 +1,4 @@ | ||
| # coding=utf-8 | ||
| # !/usr/bin/env python | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| # nidm_linreg.py | ||
| # License: Apache License, Version 2.0 | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| # Date: 07-26-22 Coded by: Ashmita Kumar ([email protected]) | ||
| # Filename: nidm_linreg.py | ||
| # | ||
| # Program description: This program provides a tool to complete a linear regression on nidm files | ||
| # | ||
| # | ||
| # ***************************************************************************** | ||
| # Development environment: Python - PyCharm IDE | ||
| # | ||
| # ***************************************************************************** | ||
| # System requirements: Python 3.X | ||
| # Libraries: os, sys, tempfile, pandas, click, nidm, csv, sklearn, numpy, statsmodel.api, patsy.contrasts | ||
| # ***************************************************************************** | ||
| # Start date: 6-15-20 | ||
| # Update history: | ||
| # DATE MODIFICATION Who | ||
| # | ||
| # | ||
| # ***************************************************************************** | ||
| # Programmer comments: | ||
| # | ||
| # | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| """This program provides a tool to complete a linear regression on nidm files""" | ||
|
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||
| import csv | ||
| import os | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,34 +1,4 @@ | ||
| #!/usr/bin/env python | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| # nidm_utils.py | ||
| # License: Apache License, Version 2.0 | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| # Date: 11-28-18 Coded by: David Keator ([email protected]) | ||
| # Filename: nidm_utils.py | ||
| # | ||
| # Program description: Tools for working with NIDM-Experiment files | ||
| # | ||
| # ***************************************************************************** | ||
| # Development environment: Python - PyCharm IDE | ||
| # | ||
| # ***************************************************************************** | ||
| # System requirements: Python 3.X | ||
| # Libraries: pybids, numpy, matplotlib, pandas, scipy, math, dateutil, datetime,argparse, | ||
| # os,sys,getopt,csv | ||
| # ***************************************************************************** | ||
| # Start date: 11-28-18 | ||
| # Update history: | ||
| # DATE MODIFICATION Who | ||
| # | ||
| # | ||
| # ***************************************************************************** | ||
| # Programmer comments: | ||
| # | ||
| # | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| """Tools for working with NIDM-Experiment files""" | ||
|
|
||
| import click | ||
| from rdflib import Graph, util | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,34 +1,4 @@ | ||
| #!/usr/bin/env python | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| # nidm_query.py | ||
| # License: Apache License, Version 2.0 | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| # Date: 8-1-18 Coded by: David Keator ([email protected]) | ||
| # Filename: nidm_query.py | ||
| # | ||
| # Program description: This program provides query functionality for NIDM-Experiment files | ||
| # | ||
| # | ||
| # ***************************************************************************** | ||
| # Development environment: Python - PyCharm IDE | ||
| # | ||
| # ***************************************************************************** | ||
| # System requirements: Python 3.X | ||
| # Libraries: os, sys, rdflib, pandas, argparse, logging | ||
| # ***************************************************************************** | ||
| # Start date: 8-1-18 | ||
| # Update history: | ||
| # DATE MODIFICATION Who | ||
| # | ||
| # | ||
| # ***************************************************************************** | ||
| # Programmer comments: | ||
| # | ||
| # | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| """This program provides query functionality for NIDM-Experiment files""" | ||
|
|
||
| from json import dumps | ||
| import os | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,34 +1,4 @@ | ||
| #!/usr/bin/env python | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| # nidm_utils.py | ||
| # License: Apache License, Version 2.0 | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| # Date: 11-28-18 Coded by: David Keator ([email protected]) | ||
| # Filename: nidm_utils.py | ||
| # | ||
| # Program description: Tools for working with NIDM-Experiment files | ||
| # | ||
| # ***************************************************************************** | ||
| # Development environment: Python - PyCharm IDE | ||
| # | ||
| # ***************************************************************************** | ||
| # System requirements: Python 3.X | ||
| # Libraries: pybids, numpy, matplotlib, pandas, scipy, math, dateutil, datetime,argparse, | ||
| # os,sys,getopt,csv | ||
| # ***************************************************************************** | ||
| # Start date: 11-28-18 | ||
| # Update history: | ||
| # DATE MODIFICATION Who | ||
| # | ||
| # | ||
| # ***************************************************************************** | ||
| # Programmer comments: | ||
| # | ||
| # | ||
| # ***************************************************************************** | ||
| # ***************************************************************************** | ||
| """ Tools for working with NIDM-Experiment files """ | ||
|
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| from argparse import ArgumentParser | ||
| import os.path | ||
|
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@dbkeator Please confirm that it is Ok to assume that this file is also under Apache 2 license (per https://github.com/incf-nidash/PyNIDM/blob/master/LICENSE) as the rest of the codebase, or it has to be GPL?