Non-parametric statistics

doc/content/specs/nidm-results_dev.html

@@ -884,6 +884,12 @@ <h1 label="nidm:MaskMap">nidm:MaskMap</h1>
                 <ul>
                     <li><span class="attribute" id="nidm:MaskMap.label">rdfs:label</span>: an                     <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> human readable description                     of the nidm:MaskMap.</li>
 
+                        <li><span class="attribute" id="nidm:MaskMap.nidm:hasMapHeader">
+                        <a>nidm:hasMapHeader</a>
+                        </span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> . (range <a>nidm:MapHeader</a>)</li> 
+                        <li><span class="attribute" id="nidm:MaskMap.nidm:inCoordinateSpace">
+                        <a>nidm:inCoordinateSpace</a>
+                        </span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> property of a DataArray to associate a CoordinateSpace with a physical file. (range <a>nidm:CoordinateSpace</a>)</li> 
                         <li><span class="attribute" id="nidm:MaskMap.nidm:isUserDefined">
                         <dfn>nidm:isUserDefined</dfn>
                         </span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> a binary flag defining whether the mask was specified by the user (true) or automatically generated during the analysis (false). (range <a title="xsd:boolean" href="http://www.w3.org/2001/XMLSchema#boolean">xsd:boolean</a>)</li>        
@@ -1447,6 +1453,12 @@ <h1 label="nidm:DisplayMaskMap">nidm:DisplayMaskMap</h1>
                 <ul>
                     <li><span class="attribute" id="nidm:DisplayMaskMap.label">rdfs:label</span>: an                     <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> human readable description                     of the nidm:DisplayMaskMap.</li>
 
+                        <li><span class="attribute" id="nidm:DisplayMaskMap.nidm:hasMapHeader">
+                        <a>nidm:hasMapHeader</a>
+                        </span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> . (range <a>nidm:MapHeader</a>)</li> 
+                        <li><span class="attribute" id="nidm:DisplayMaskMap.nidm:inCoordinateSpace">
+                        <a>nidm:inCoordinateSpace</a>
+                        </span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> property of a DataArray to associate a CoordinateSpace with a physical file. (range <a>nidm:CoordinateSpace</a>)</li> 
                         <li><span class="attribute" id="nidm:DisplayMaskMap.nidm:isUserDefined">
                         <a>nidm:isUserDefined</a>
                         </span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> a binary flag defining whether the mask was specified by the user (true) or automatically generated during the analysis (false). (range <a title="xsd:boolean" href="http://www.w3.org/2001/XMLSchema#boolean">xsd:boolean</a>)</li>        
@@ -1642,6 +1654,15 @@ <h1 label="nidm:SearchSpaceMaskMap">nidm:SearchSpaceMaskMap</h1>
                 <ul>
                     <li><span class="attribute" id="nidm:SearchSpaceMaskMap.label">rdfs:label</span>: an                     <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> human readable description                     of the nidm:SearchSpaceMaskMap.</li>
 
+                        <li><span class="attribute" id="nidm:SearchSpaceMaskMap.nidm:hasMapHeader">
+                        <a>nidm:hasMapHeader</a>
+                        </span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> . (range <a>nidm:MapHeader</a>)</li> 
+                        <li><span class="attribute" id="nidm:SearchSpaceMaskMap.nidm:inCoordinateSpace">
+                        <a>nidm:inCoordinateSpace</a>
+                        </span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> property of a DataArray to associate a CoordinateSpace with a physical file. (range <a>nidm:CoordinateSpace</a>)</li> 
+                        <li><span class="attribute" id="nidm:SearchSpaceMaskMap.nidm:isUserDefined">
+                        <a>nidm:isUserDefined</a>
+                        </span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> a binary flag defining whether the mask was specified by the user (true) or automatically generated during the analysis (false). (range <a title="xsd:boolean" href="http://www.w3.org/2001/XMLSchema#boolean">xsd:boolean</a>)</li> 
                         <li><span class="attribute" id="nidm:SearchSpaceMaskMap.nidm:randomFieldStationarity">
                         <dfn>nidm:randomFieldStationarity</dfn>
                         </span>: an <em class="rfc2119" title="OPTIONAL">OPTIONAL</em> is the random field assumed to be stationary across the entire search volume?. (range <a title="xsd:boolean" href="http://www.w3.org/2001/XMLSchema#boolean">xsd:boolean</a>)</li> 

nidm/nidm-results/extensions/non_parametric/scripts/create_spm_example_nonparam.py

@@ -0,0 +1,66 @@
+"""
+Create SPM example 005 stored in nidm/nidm-results/spm/example005 by using the 
+class templates available in nidm/nidm-results/terms/templates
+
+@author: Camille Maumet <[email protected]>
+@copyright: University of Warwick 2013-2014
+"""
+import os
+from create_example_from_templates import ExampleFromTemplate
+
+RELPATH = os.path.dirname(os.path.abspath(__file__))
+
+def main():
+	nidm_classes = {
+		"StatisticMap_PseudoT": dict(
+			var_smoothing="[6 6 6]",
+			statistic_map_id="niiri:statistic_map_id",
+			label="Smoothed Variance T-Statistic Map: passive listening > rest",
+			location="file://./SmoothedVarianceTStatistic.nii.gz",
+			format="image/nifti",
+			filename="SmoothedVarianceTStatistic.nii.gz",
+			statistic_type="nidm:SmoothedVarianceTStatistic",
+			stat_type_comment="",
+			contrast_name="passive listening > rest",
+			effect_dof="1",
+			sha="799e9bbf8c15b35c0098bca4",
+			coordinate_space_id="niiri:coordinate_space_id_1",
+			contrast_est_id="niiri:contrast_estimation_id"
+			),
+		"InferenceUsedNonParam": dict(
+			inference_id="niiri:inference_id_1",
+			label="Inference",
+			alternative_hyp="nidm:OneTailedTest",
+			is_parametric="false",
+			non_param_dist_id="niiri:non_parametric_null_dististribution_id",
+			statistic_map_id="niiri:statistic_map_id"
+			),
+		"NonParametricDistribution": dict(
+			non_param_dist_id="niiri:non_parametric_null_dististribution_id",
+			label="Non-Parametric Null Distribution",
+			n_perms="5000",
+			exchangeability_blocks="4"
+			),
+		"CoordinateSpace": dict(
+			coordinate_space_id="niiri:coordinate_space_id_1",
+			label="Coordinate space 1",
+			voxel_to_world_mapping="[[-3, 0, 0, 78],[0, 3, 0, -112],[0, 0, 3, -70],[0, 0, 0, 1]]",
+			voxel_units="['mm', 'mm', 'mm']",
+			voxel_size="[3, 3, 3]",
+			coord_system="nidm:MNICoordinateSystem",
+			number_of_dim="3",
+			dimensions="[53,63,52]")
+	}
+
+	NIDM_SPM_DIR = os.path.join(os.path.dirname(
+        os.path.dirname(os.path.abspath(__file__))), 'spm', "example001")
+	ttl_file = os.path.join(NIDM_SPM_DIR, 'spm_nonparametric.ttl')
+
+	EXT_PATH = os.path.dirname(RELPATH)
+	EXTENSION_TPL_DIR = os.path.join(EXT_PATH, "terms", "templates")
+
+	example = ExampleFromTemplate(nidm_classes, ttl_file, False, EXTENSION_TPL_DIR)
+	example.create_example()
+
+if __name__ == '__main__':
+	main()

nidm/nidm-results/extensions/non_parametric/spm/example001/README.md

@@ -0,0 +1,9 @@
+
+Prov store: https://provenance.ecs.soton.ac.uk/store/documents/76838/
+
+Alternative serialisations: [json](https://provenance.ecs.soton.ac.uk/store/documents/76838.json), [turtle](https://provenance.ecs.soton.ac.uk/store/documents/76838.ttl), 
+Graph: [svg](https://provenance.ecs.soton.ac.uk/store/documents/76838.svg), [PDF](https://provenance.ecs.soton.ac.uk/store/documents/76838.pdf), [png](https://provenance.ecs.soton.ac.uk/store/documents/76838.png)
+
+![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/76838.png)
+
+

nidm/nidm-results/extensions/non_parametric/spm/example001/spm_nonparametric.provn

@@ -0,0 +1,24 @@
+document
+prefix crypto <http://id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#>
+prefix neurolex <http://neurolex.org/wiki/>
+prefix obo <http://purl.obolibrary.org/obo/>
+prefix dct <http://purl.org/dc/terms/>
+prefix spm <http://www.incf.org/ns/nidash/spm#>
+prefix pre_0 <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+prefix fsl <http://www.incf.org/ns/nidash/fsl#>
+prefix rdfs <http://www.w3.org/2000/01/rdf-schema#>
+prefix nfo <http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#>
+prefix nidm <http://www.incf.org/ns/nidash/nidm#>
+prefix niiri <http://iri.nidash.org/>
+prefix xsd <http://www.w3.org/2001/XMLSchema>
+prefix bnode <http://openprovenance.org/provtoolbox/bnode/>
+prefix dctype <http://purl.org/dc/dcmitype/>
+prefix dc <http://purl.org/dc/elements/1.1/>
+activity(niiri:inference_id_1,-,-,[prov:type = 'nidm:Inference', prov:label = "Inference", nidm:isParametricTest = "false" %% xsd:boolean, nidm:hasAlternativeHypothesis = 'nidm:OneTailedTest'])
+entity(niiri:non_parametric_null_dististribution_id,[prov:type = 'nidm:NonParametricNullDistribution', prov:label = "Non-Parametric Null Distribution", nidm:numberOfPermutations = "5000" %% xsd:int, nidm:exchangeabilityBlockSize = "4" %% xsd:int])
+entity(niiri:statistic_map_id,[prov:type = 'nidm:StatisticMap', prov:label = "Smoothed Variance T-Statistic Map: passive listening > rest", prov:location = "file://./SmoothedVarianceTStatistic.nii.gz" %% xsd:anyURI, nidm:statisticType = 'nidm:SmoothedVarianceTStatistic', nfo:fileName = "SmoothedVarianceTStatistic.nii.gz" %% xsd:string, dct:format = "image/nifti" %% xsd:string, nidm:contrastName = "passive listening > rest" %% xsd:string, nidm:effectDegreesOfFreedom = "1" %% xsd:float, nidm:inCoordinateSpace = 'niiri:coordinate_space_id_1', crypto:sha512 = "799e9bbf8c15b35c0098bca4" %% xsd:string, nidm:varianceSmoothingFWHM = "[6 6 6]" %% xsd:string])
+entity(niiri:coordinate_space_id_1,[prov:type = 'nidm:CoordinateSpace', prov:label = "Coordinate space 1", nidm:voxelToWorldMapping = "[[-3, 0, 0, 78],[0, 3, 0, -112],[0, 0, 3, -70],[0, 0, 0, 1]]" %% xsd:string, nidm:voxelUnits = "['mm', 'mm', 'mm']" %% xsd:string, nidm:voxelSize = "[3, 3, 3]" %% xsd:string, nidm:inWorldCoordinateSystem = 'nidm:MNICoordinateSystem', nidm:numberOfDimensions = "3" %% xsd:int, nidm:dimensionsInVoxels = "[53,63,52]" %% xsd:string])
+used(niiri:inference_id_1,niiri:non_parametric_null_dististribution_id,-)
+used(niiri:inference_id_1,niiri:statistic_map_id,-)
+wasGeneratedBy(niiri:statistic_map_id,niiri:contrast_estimation_id,-)
+endDocument

nidm/nidm-results/extensions/non_parametric/spm/example001/spm_nonparametric.ttl

@@ -0,0 +1,50 @@
+@prefix prov: <http://www.w3.org/ns/prov#> .
+@prefix crypto: <http://id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#> .
+@prefix neurolex: <http://neurolex.org/wiki/> .
+@prefix dc: <http://purl.org/dc/elements/1.1/> .
+@prefix dct: <http://purl.org/dc/terms/> .
+@prefix dctype: <http://purl.org/dc/dcmitype/> .
+@prefix spm: <http://www.incf.org/ns/nidash/spm#> .
+@prefix fsl: <http://www.incf.org/ns/nidash/fsl#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix nidm: <http://www.incf.org/ns/nidash/nidm#> .
+@prefix niiri: <http://iri.nidash.org/> .
+@prefix nfo: <http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix obo: <http://purl.obolibrary.org/obo/> .
+
+
+
+niiri:coordinate_space_id_1 a prov:Entity , nidm:CoordinateSpace ;
+	rdfs:label "Coordinate space 1" ;
+	nidm:voxelToWorldMapping "[[-3, 0, 0, 78],[0, 3, 0, -112],[0, 0, 3, -70],[0, 0, 0, 1]]"^^xsd:string ;
+	nidm:voxelUnits "['mm', 'mm', 'mm']"^^xsd:string ;
+	nidm:voxelSize "[3, 3, 3]"^^xsd:string ;
+	nidm:inWorldCoordinateSystem nidm:MNICoordinateSystem ;
+	nidm:numberOfDimensions "3"^^xsd:int ;
+	nidm:dimensionsInVoxels "[53,63,52]"^^xsd:string .
+
+niiri:inference_id_1 a prov:Activity , nidm:Inference ;
+	rdfs:label "Inference" ;
+    nidm:isParametricTest "false"^^xsd:boolean ;
+	nidm:hasAlternativeHypothesis nidm:OneTailedTest ;
+    prov:used niiri:non_parametric_null_dististribution_id, niiri:statistic_map_id .
+
+niiri:non_parametric_null_dististribution_id a prov:Entity , nidm:NonParametricNullDistribution;
+	rdfs:label "Non-Parametric Null Distribution" ;
+	nidm:numberOfPermutations "5000"^^xsd:int ;
+	nidm:exchangeabilityBlockSize "4"^^xsd:int .
+
+niiri:statistic_map_id a prov:Entity , nidm:StatisticMap ;
+	rdfs:label "Smoothed Variance T-Statistic Map: passive listening > rest" ;
+	prov:atLocation "file://./SmoothedVarianceTStatistic.nii.gz"^^xsd:anyURI ;
+	nidm:statisticType nidm:SmoothedVarianceTStatistic ; # 
+	nfo:fileName "SmoothedVarianceTStatistic.nii.gz"^^xsd:string ;
+	dct:format "image/nifti"^^xsd:string ;
+	nidm:contrastName "passive listening > rest"^^xsd:string ;
+	nidm:effectDegreesOfFreedom "1"^^xsd:float ;
+	nidm:inCoordinateSpace niiri:coordinate_space_id_1 ;
+	crypto:sha512 "799e9bbf8c15b35c0098bca4"^^xsd:string ;
+	prov:wasGeneratedBy niiri:contrast_estimation_id;
+	nidm:varianceSmoothingFWHM "[6 6 6]"^^xsd:string .
+

nidm/nidm-results/extensions/non_parametric/terms/catalog-v001.xml

@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
+    <uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/nidm/nidmresults.owl" uri="../../../terms/nidm-results.owl"/>
+    <group id="Folder Repository, directory=, recursive=true, Auto-Update=true, version=2" prefer="public" xml:base=""/>
+    <uri id="Imports Wizard Entry" name="http://purl.org/nidash/nidm/nfo_import.owl" uri="../../../../imports/nfo_import.ttl"/>
+    <uri id="Imports Wizard Entry" name="http://purl.org/nidash/nidm/dc_import.owl" uri="../../../../imports/dc_import.ttl"/>
+    <uri id="Imports Wizard Entry" name="http://purl.org/nidash/nidm/stato_import.owl" uri="../../../../imports/stato_import.ttl"/>
+    <uri id="Imports Wizard Entry" name="http://www.w3.org/ns/prov-o-20130430" uri="http://www.w3.org/ns/prov-o-20130430"/>
+    <uri id="Imports Wizard Entry" name="http://purl.obolibrary.org/nidm/iao_import.owl" uri="../../../../imports/iao_import.ttl"/>
+</catalog>