[TEST] testing json and markdown export for team description

narps_open/data/description/__main__.py

@@ -49,3 +49,5 @@
         print(dumps(information.categorized_for_analysis, indent = 4))
     elif arguments.dictionary == 'derived':
         print(dumps(information.derived, indent = 4))
+    else:
+        print(dumps(information, indent = 4))

tests/data/test_description.py

@@ -11,8 +11,11 @@
     pytest -q test_description.py -k <selected_test>
 """
 
+from os.path import join
+
 from pytest import raises, mark
 
+from narps_open.utils.configuration import Configuration
 from narps_open.data.description import TeamDescription
 
 class TestUtilsDescription:
@@ -86,3 +89,36 @@ def test_arguments_properties():
         assert description['general.softwares'] == 'FSL 5.0.11, MRIQC, FMRIPREP'
         assert isinstance(description.general, dict)
         assert description.general['softwares'] == 'FSL 5.0.11, MRIQC, FMRIPREP'
+
+    @staticmethod
+    @mark.unit_test
+    def test_markdown():
+        """ Test writing a TeamDescription as Markdown """
+
+        # Generate markdown from description
+        description = TeamDescription('9Q6R')
+        markdown = description.markdown()
+
+        # Compare markdown with test file
+        test_file_path = join(
+            Configuration()['directories']['test_data'],
+            'data', 'description', 'test_markdown.md'
+            )
+        with open(test_file_path, 'r', encoding = 'utf-8') as file:
+            assert markdown == file.read()
+
+    @staticmethod
+    @mark.unit_test
+    def test_str():
+        """ Test writing a TeamDescription as JSON """
+
+        # Generate report
+        description = TeamDescription('9Q6R')
+
+        # Compare string version of the description with test file
+        test_file_path = join(
+            Configuration()['directories']['test_data'],
+            'data', 'description', 'test_str.json'
+            )
+        with open(test_file_path, 'r', encoding = 'utf-8') as file:
+            assert str(description) == file.read()

tests/data/test_results.py

@@ -103,7 +103,8 @@ def test_rectify():
         """ Test the rectify method """
 
         # Get raw data
-        orig_directory = join(Configuration()['directories']['test_data'], 'results', 'team_2T6S')
+        orig_directory = join(
+            Configuration()['directories']['test_data'], 'data', 'results', 'team_2T6S')
 
         # Create test data
         test_directory = join(Configuration()['directories']['test_runs'], 'results_team_2T6S')

tests/test_data/data/description/test_markdown.md

@@ -0,0 +1,98 @@
+# NARPS team description : 9Q6R
+## General
+* `teamID` : 9Q6R
+* `NV_collection_link` : https://neurovault.org/collections/4765/
+* `results_comments` : Note: Amygdala wasn't recruited for hypothesis tests 7-9, but the extended salience network was recruited in all contrasts (e.g. aINS, ACC). Based on looking at the unthresholded maps, hypotheses 8 and 9 would've been confirmed at lower cluster thresholds (i.e. z≥2.3 rather than z≥3.1).
+* `preregistered` : No
+* `link_preregistration_form` : NA
+* `regions_definition` : Harvard-Oxford probabilistic cortical and subcortical atlases (Frontal Median Cortex, L+R Amyg, and L+R Accum for vmPFC, amyg, and VS, respectively). Also used Neurosynth to generate a mask based on the search term "ventral striatum" (height threshold at z>12, and cluster-extent at > 400mm^3)
+* `softwares` : FSL 5.0.11, MRIQC, FMRIPREP
+* `general_comments` : NA
+## Exclusions
+* `n_participants` : 104
+* `exclusions_details` : N=104 (54 eq_indiff, 50 eq_range). Excluded sub-018, sub-030, sub-088, and sub-100. High motion during function runs: All four participants had at least one run where > 50% of the TRs contained FD > 0.2mm. 18, 30, and 100 in particular were constant movers (all 4 runs > 50% TRS > 0.2 mm FD) 
+## Preprocessing
+* `used_fmriprep_data` : No
+* `preprocessing_order` :  - MRIQC and FMRIPREP run on a local HPC
+- FSL used for mass univariate analyses, avoiding re-registration using this approach: https://www.youtube.com/watch?time_continue=7&v=U3tG7JMEf7M
+* `brain_extraction` : Freesurfer (i.e. part of fmriprep default pipeline)
+* `segmentation` : Freesurfer
+* `slice_time_correction` : Not performed
+* `motion_correction` : Framewise displacement, and six standard motion regressors (x, y, z, rotx, rotx, and rotz) within subjects.; generated via MRIQC 
+* `motion` : 6
+* `gradient_distortion_correction` : NA
+* `intra_subject_coreg` : bbregister, flirt, default FMRIPREP
+* `distortion_correction` : Fieldmap-less distortion correction within fmriprep pipeline (--use-syn-sdc)
+* `inter_subject_reg` : ANTs, multiscale nonlinear mutual-information default within FMRIPREP pipeline.
+* `intensity_correction` : Default fMRIPREP INU correction
+* `intensity_normalization` : Default fMRIPREP INU normalization
+* `noise_removal` : None
+* `volume_censoring` : None
+* `spatial_smoothing` : 5mm FWHM
+* `preprocessing_comments` : NA
+## Analysis
+* `data_submitted_to_model` : 453 total volumes, 104 participants (54 eq_indiff, 50 eq_range)
+* `spatial_region_modeled` : Whole-Brain
+* `independent_vars_first_level` : Event-related design predictors:
+- Modeled duration = 4
+- EVs  (3): Mean-centered Gain, Mean-Centered Loss, Events (constant)
+Block design:
+- baseline not explicitly modeled
+HRF:
+- FMRIB's Linear Optimal Basis Sets
+Movement regressors:
+- FD, six parameters (x, y, z, RotX, RotY, RotZ)
+* `RT_modeling` : none
+* `movement_modeling` : 1
+* `independent_vars_higher_level` : EVs (2): eq_indiff, eq_range
+Contrasts in the group-level design matrix:
+1 --> mean (1, 1)
+2 --> eq_indiff (1, 0)
+3 --> eq_range (0, 1)
+4 --> indiff_gr_range (1, -1)
+5 --> range_gr_indiff (-1, 1)
+* `model_type` : Mass Univariate
+* `model_settings` : First model: individual runs; 
+Second model: higher-level analysis on lower-level FEAT directories in a fixed effects model at the participant-level; 
+Third model: higher-level analysis on 3D COPE images from *.feat directories within second model *.gfeat; FLAME 1 (FMRIB's Local Analysis of Mixed Effects), with a cluster threshold of z≥3.1
+* `inference_contrast_effect` : First-Level A (Run-level; not listed: linear basis functions, FSL FLOBs):
+Model EVs (3): gain, loss, event
+- COPE1: Pos Gain (1, 0, 0)
+- COPE4: Neg Gain  (-1, 0, 0)
+- COPE7: Pos Loss (0, 1, 0)
+- COPE10: Neg Loss (0, -1, 0)
+- COPE13: Events (0, 0, 1)
+Confound EVs (7): Framewise Displacement, x, y, z, RotX, RotY, RotZ. Generated in MRIQC.
+
+First-Level B (Participant-level):
+- All COPEs from the runs modeled in a high-level FEAT fixed effect model
+
+Second-Level (Group-level):
+- Separate high-level FLAME 1 models run on COPE1, COPE4, COPE7, and COPE10. Hypotheses 1-4 answered using the COPE1 model, Hypotheses 5-6 answered using the COPE10 model, and Hypotheses 7-9 answered using the COPE7 model.
+Model EVs (2): eq_indiff, eq_range
+- mean (1, 1)
+- eq_indiff (1, 0)
+- eq_range (0, 1)
+- indiff_gr_range (1, -1)
+- range_gr_indiff (-1, 1) 
+* `search_region` : Whole brain
+* `statistic_type` : Cluster size
+* `pval_computation` : Standard parametric inference
+* `multiple_testing_correction` : GRF_theory based FEW correction at z≥3.1 in FSL
+* `comments_analysis` : NA
+## Categorized for analysis
+* `region_definition_vmpfc` : atlas HOA
+* `region_definition_striatum` : atlas HOA, neurosynth
+* `region_definition_amygdala` : atlas HOA
+* `analysis_SW` : FSL
+* `analysis_SW_with_version` : FSL 5.0.11
+* `smoothing_coef` : 5
+* `testing` : parametric
+* `testing_thresh` : p<0.001
+* `correction_method` : GRTFWE cluster
+* `correction_thresh_` : p<0.05
+## Derived
+* `n_participants` : 104
+* `excluded_participants` : 018, 030, 088, 100
+* `func_fwhm` : 5
+* `con_fwhm` : 

tests/test_data/data/description/test_str.json

@@ -0,0 +1,57 @@
+{
+    "general.teamID": "9Q6R",
+    "general.NV_collection_link": "https://neurovault.org/collections/4765/",
+    "general.results_comments": "Note: Amygdala wasn't recruited for hypothesis tests 7-9, but the extended salience network was recruited in all contrasts (e.g. aINS, ACC). Based on looking at the unthresholded maps, hypotheses 8 and 9 would've been confirmed at lower cluster thresholds (i.e. z\u22652.3 rather than z\u22653.1).",
+    "general.preregistered": "No",
+    "general.link_preregistration_form": "NA",
+    "general.regions_definition": "Harvard-Oxford probabilistic cortical and subcortical atlases (Frontal Median Cortex, L+R Amyg, and L+R Accum for vmPFC, amyg, and VS, respectively). Also used Neurosynth to generate a mask based on the search term \"ventral striatum\" (height threshold at z>12, and cluster-extent at > 400mm^3)",
+    "general.softwares": "FSL 5.0.11, MRIQC, FMRIPREP",
+    "exclusions.n_participants": "104",
+    "exclusions.exclusions_details": "N=104 (54 eq_indiff, 50 eq_range). Excluded sub-018, sub-030, sub-088, and sub-100. High motion during function runs: All four participants had at least one run where > 50% of the TRs contained FD > 0.2mm. 18, 30, and 100 in particular were constant movers (all 4 runs > 50% TRS > 0.2 mm FD) ",
+    "preprocessing.used_fmriprep_data": "No",
+    "preprocessing.preprocessing_order": " - MRIQC and FMRIPREP run on a local HPC\n- FSL used for mass univariate analyses, avoiding re-registration using this approach: https://www.youtube.com/watch?time_continue=7&v=U3tG7JMEf7M",
+    "preprocessing.brain_extraction": "Freesurfer (i.e. part of fmriprep default pipeline)",
+    "preprocessing.segmentation": "Freesurfer",
+    "preprocessing.slice_time_correction": "Not performed",
+    "preprocessing.motion_correction": "Framewise displacement, and six standard motion regressors (x, y, z, rotx, rotx, and rotz) within subjects.; generated via MRIQC ",
+    "preprocessing.motion": "6",
+    "preprocessing.gradient_distortion_correction": "NA",
+    "preprocessing.intra_subject_coreg": "bbregister, flirt, default FMRIPREP",
+    "preprocessing.distortion_correction": "Fieldmap-less distortion correction within fmriprep pipeline (--use-syn-sdc)",
+    "preprocessing.inter_subject_reg": "ANTs, multiscale nonlinear mutual-information default within FMRIPREP pipeline.",
+    "preprocessing.intensity_correction": "Default fMRIPREP INU correction",
+    "preprocessing.intensity_normalization": "Default fMRIPREP INU normalization",
+    "preprocessing.noise_removal": "None",
+    "preprocessing.volume_censoring": "None",
+    "preprocessing.spatial_smoothing": "5mm FWHM",
+    "preprocessing.preprocessing_comments": "NA",
+    "analysis.data_submitted_to_model": "453 total volumes, 104 participants (54 eq_indiff, 50 eq_range)",
+    "analysis.spatial_region_modeled": "Whole-Brain",
+    "analysis.independent_vars_first_level": "Event-related design predictors:\n- Modeled duration = 4\n- EVs  (3): Mean-centered Gain, Mean-Centered Loss, Events (constant)\nBlock design:\n- baseline not explicitly modeled\nHRF:\n- FMRIB's Linear Optimal Basis Sets\nMovement regressors:\n- FD, six parameters (x, y, z, RotX, RotY, RotZ)",
+    "analysis.RT_modeling": "none",
+    "analysis.movement_modeling": "1",
+    "analysis.independent_vars_higher_level": "EVs (2): eq_indiff, eq_range\nContrasts in the group-level design matrix:\n1 --> mean (1, 1)\n2 --> eq_indiff (1, 0)\n3 --> eq_range (0, 1)\n4 --> indiff_gr_range (1, -1)\n5 --> range_gr_indiff (-1, 1)",
+    "analysis.model_type": "Mass Univariate",
+    "analysis.model_settings": "First model: individual runs; \nSecond model: higher-level analysis on lower-level FEAT directories in a fixed effects model at the participant-level; \nThird model: higher-level analysis on 3D COPE images from *.feat directories within second model *.gfeat; FLAME 1 (FMRIB's Local Analysis of Mixed Effects), with a cluster threshold of z\u22653.1",
+    "analysis.inference_contrast_effect": "First-Level A (Run-level; not listed: linear basis functions, FSL FLOBs):\nModel EVs (3): gain, loss, event\n- COPE1: Pos Gain (1, 0, 0)\n- COPE4: Neg Gain  (-1, 0, 0)\n- COPE7: Pos Loss (0, 1, 0)\n- COPE10: Neg Loss (0, -1, 0)\n- COPE13: Events (0, 0, 1)\nConfound EVs (7): Framewise Displacement, x, y, z, RotX, RotY, RotZ. Generated in MRIQC.\n\nFirst-Level B (Participant-level):\n- All COPEs from the runs modeled in a high-level FEAT fixed effect model\n\nSecond-Level (Group-level):\n- Separate high-level FLAME 1 models run on COPE1, COPE4, COPE7, and COPE10. Hypotheses 1-4 answered using the COPE1 model, Hypotheses 5-6 answered using the COPE10 model, and Hypotheses 7-9 answered using the COPE7 model.\nModel EVs (2): eq_indiff, eq_range\n- mean (1, 1)\n- eq_indiff (1, 0)\n- eq_range (0, 1)\n- indiff_gr_range (1, -1)\n- range_gr_indiff (-1, 1) ",
+    "analysis.search_region": "Whole brain",
+    "analysis.statistic_type": "Cluster size",
+    "analysis.pval_computation": "Standard parametric inference",
+    "analysis.multiple_testing_correction": "GRF_theory based FEW correction at z\u22653.1 in FSL",
+    "analysis.comments_analysis": "NA",
+    "general.general_comments": "NA",
+    "categorized_for_analysis.region_definition_vmpfc": "atlas HOA",
+    "categorized_for_analysis.region_definition_striatum": "atlas HOA, neurosynth",
+    "categorized_for_analysis.region_definition_amygdala": "atlas HOA",
+    "categorized_for_analysis.analysis_SW": "FSL",
+    "categorized_for_analysis.analysis_SW_with_version": "FSL 5.0.11",
+    "categorized_for_analysis.smoothing_coef": "5",
+    "categorized_for_analysis.testing": "parametric",
+    "categorized_for_analysis.testing_thresh": "p<0.001",
+    "categorized_for_analysis.correction_method": "GRTFWE cluster",
+    "categorized_for_analysis.correction_thresh_": "p<0.05",
+    "derived.n_participants": "104",
+    "derived.excluded_participants": "018, 030, 088, 100",
+    "derived.func_fwhm": "5",
+    "derived.con_fwhm": ""
+}