8000 Change AutoContrasts to DummyContrasts by adelavega · Pull Request #197 · poldracklab/fitlins · GitHub
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Change AutoContrasts to DummyContrasts #197

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Merged
merged 6 commits into from
Nov 15, 2019
Merged

Change AutoContrasts to DummyContrasts #197

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7c4de26
Change AutoContrasts to DummyContrasts
adelavega Nov 12, 2019
176b175
PIN: Pybids
adelavega Nov 14, 2019
446d581
Pin to fixed version
adelavega Nov 14, 2019
7da47d3
Fix example models
adelavega Nov 14, 2019
736d2b0
Update notebook
adelavega Nov 14, 2019
f0ede0c
Bump pybids PIN
adelavega Nov 15, 2019
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2 changes: 1 addition & 1 deletion docs/examples/models.rst
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Expand Up @@ -20,7 +20,7 @@ The ``Model.X`` section demonstrates selection of regressors for the design
matrix, and ``Contrasts`` shows how to perform a simple contrast between
two conditions.

At the ``dataset`` level, the ``AutoContrasts`` option demonstrates taking
At the ``dataset`` level, the ``DummyContrasts`` option demonstrates taking
a simple mean at the group level.

.. raw:: html
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2 changes: 1 addition & 1 deletion docs/model.rst
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Expand Up @@ -123,7 +123,7 @@ In this case, we can use an ``AutoContrast`` to make a very simple final step:

{
"Level": "Dataset",
"AutoContrasts": ["a_vs_b"]
"DummyContrasts": ["a_vs_b"]
}

This is equivalent to the more verbose:
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10 changes: 8 additions & 2 deletions examples/models/ds000003/models/model-001_smdl.json
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Expand Up @@ -30,7 +30,10 @@
"a_comp_cor_03", "a_comp_cor_04", "a_comp_cor_05"
]
},
"AutoContrasts": ["trial_type.word", "trial_type.pseudoword"],
"DummyContrasts": {
"Conditions": ["trial_type.word", "trial_type.pseudoword"],
"Type": "t"
},
"Contrasts": [
{
"Name": "word_gt_pseudo",
Expand All @@ -54,7 +57,10 @@
},
{
"Level": "dataset",
"AutoContrasts": ["word_gt_pseudo", "task_vs_baseline"],
"DummyContrasts": {
"Conditions": ["word_gt_pseudo", "task_vs_baseline"],
"Type": "t"
},
"Contrasts":[
{
"Name": "any_words",
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5 changes: 4 additions & 1 deletion examples/models/ds000030/models/model-001_smdl.json
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Expand Up @@ -62,7 +62,10 @@
},
{
"Level": "dataset",
"AutoContrasts": ["accept_vs_explode"]
"DummyContrasts": {
"Conditions": ["accept_vs_explode"],
"Type": "t"
}
}
]
}
5 changes: 4 additions & 1 deletion examples/models/ds000114/models/model-001_smdl.json
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Expand Up @@ -81,7 +81,10 @@
},
{
"Level": "dataset",
"AutoContrasts": ["session_diff"]
"DummyContrasts": {
"Conditions": ["session_diff"],
"Type": "t"
}
}
]
}
10 changes: 8 additions & 2 deletions examples/models/ds000117/models/model-001_smdl.json
E30A
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Expand Up @@ -51,11 +51,17 @@
},
{
"Level": "subject",
"AutoContrasts": ["face_vs_scram"]
"DummyContrasts": {
"Conditions": ["face_vs_scram"],
"Type": "FEMA"
}
},
{
"Level": "dataset",
"AutoContrasts": ["face_vs_scram"]
"DummyContrasts": {
"Conditions": ["face_vs_scram"],
"Type": "t"
}
}
]
}
161 changes: 94 additions & 67 deletions examples/notebooks/ds003_sample_analysis.ipynb
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Expand Up @@ -312,72 +312,93 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"{\n",
" \"Name\": \"ds003_model001\",\n",
" \"Description\": \"\",\n",
" \"Input\": {\n",
" \"task\": \"rhymejudgment\"\n",
" },\n",
" \"Steps\": [\n",
" {\n",
" \"Level\": \"run\",\n",
" \"Transformations\": [\n",
" {\n",
" \"Name\": \"Factor\",\n",
" \"Input\": [\n",
" \"trial_type\"\n",
" ]\n",
" },\n",
" {\n",
" \"Name\": \"Convolve\",\n",
" \"Input\": [\"trial_type.word\", \"trial_type.pseudoword\"],\n",
" \"Model\": \"spm\"\n",
" }\n",
" ],\n",
" \"Model\": {\n",
" \"X\": [\n",
" \"trial_type.word\",\n",
" \"trial_type.pseudoword\",\n",
" \"framewise_displacement\",\n",
" \"tran 28BE s_x\", \"trans_y\", \"trans_z\", \"rot_x\", \"rot_y\", \"rot_z\",\n",
" \"a_comp_cor_00\", \"a_comp_cor_01\", \"a_comp_cor_02\",\n",
" \"a_comp_cor_03\", \"a_comp_cor_04\", \"a_comp_cor_05\"\n",
" ]\n",
" },\n",
" \"Contrasts\": [\n",
" {\n",
" \"Name\": \"word_gt_pseudo\",\n",
" \"ConditionList\": [\n",
" \"trial_type.word\",\n",
" \"trial_type.pseudoword\"\n",
" ],\n",
" \"Weights\": [1, -1],\n",
" \"Type\": \"t\"\n",
" },\n",
" {\n",
" \"Name\": \"task_vs_baseline\",\n",
" \"ConditionList\": [\n",
" \"trial_type.word\",\n",
" \"trial_type.pseudoword\"\n",
" ],\n",
" \"Weights\": [0.5, 0.5],\n",
" \"Type\": \"t\"\n",
" }\n",
" ]\n",
" },\n",
" {\n",
" \"Level\": \"dataset\",\n",
" \"AutoContrasts\": [\"word_gt_pseudo\", \"task_vs_baseline\"]\n",
" }\n",
" ]\n",
"}\n"
"{\r\n",
" \"Name\": \"ds003_model001\",\r\n",
" \"Description\": \"\",\r\n",
" \"Input\": {\r\n",
" \"task\": \"rhymejudgment\"\r\n",
" },\r\n",
" \"Steps\": [\r\n",
" {\r\n",
" \"Level\": \"run\",\r\n",
" \"Transformations\": [\r\n",
" {\r\n",
" \"Name\": \"Factor\",\r\n",
" \"Input\": [\r\n",
" \"trial_type\"\r\n",
" ]\r\n",
" },\r\n",
" {\r\n",
" \"Name\": \"Convolve\",\r\n",
" \"Input\": [\"trial_type.word\", \"trial_type.pseudoword\"],\r\n",
" \"Model\": \"spm\"\r\n",
" }\r\n",
" ],\r\n",
" \"Model\": {\r\n",
" \"X\": [\r\n",
" \"trial_type.word\",\r\n",
" \"trial_type.pseudoword\",\r\n",
" \"framewise_displacement\",\r\n",
" \"trans_x\", \"trans_y\", \"trans_z\", \"rot_x\", \"rot_y\", \"rot_z\",\r\n",
" \"a_comp_cor_00\", \"a_comp_cor_01\", \"a_comp_cor_02\",\r\n",
" \"a_comp_cor_03\", \"a_comp_cor_04\", \"a_comp_cor_05\"\r\n",
" ]\r\n",
" },\r\n",
" \"DummyContrasts\": {\r\n",
" \"Conditions\": [\"trial_type.word\", \"trial_type.pseudoword\"],\r\n",
" \"Type\": \"t\"\r\n",
" },\r\n",
" \"Contrasts\": [\r\n",
" {\r\n",
" \"Name\": \"word_gt_pseudo\",\r\n",
" \"ConditionList\": [\r\n",
" \"trial_type.word\",\r\n",
" \"trial_type.pseudoword\"\r\n",
" ],\r\n",
" \"Weights\": [1, -1],\r\n",
" \"Type\": \"t\"\r\n",
" },\r\n",
" {\r\n",
" \"Name\": \"task_vs_baseline\",\r\n",
" \"ConditionList\": [\r\n",
" \"trial_type.word\",\r\n",
" \"trial_type.pseudoword\"\r\n",
" ],\r\n",
" \"Weights\": [0.5, 0.5],\r\n",
" \"Type\": \"t\"\r\n",
" }\r\n",
" ]\r\n",
" },\r\n",
" {\r\n",
" \"Level\": \"dataset\",\r\n",
" \"DummyContrasts\": {\r\n",
" \"Conditions\": [\"word_gt_pseudo\", \"task_vs_baseline\"],\r\n",
" \"Type\": \"t\"\r\n",
" },\r\n",
" \"Contrasts\":[\r\n",
" {\r\n",
" \"Name\": \"any_words\",\r\n",
" \"ConditionList\": [\r\n",
" \"trial_type.word\",\r\n",
" \"trial_type.pseudoword\"\r\n",
" ],\r\n",
" \"Weights\": [\r\n",
" [1, 0],\r\n",
" [0, 1]\r\n",
" ],\r\n",
" \"Type\": \"F\"\r\n",
" }\r\n",
" ]\r\n",
" }\r\n",
" ]\r\n",
"}\r\n"
]
}
],
Expand Down Expand Up @@ -2999,15 +3020,21 @@
],
"metadata": {
"kernelspec": {
"display_name": "Bash",
"language": "bash",
"name": "bash"
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": "shell",
"file_extension": ".sh",
"mimetype": "text/x-sh",
"name": "bash"
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.8"
},
"sos": {
"kernels": [
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2 changes: 1 addition & 1 deletion setup.cfg
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Expand Up @@ -29,7 +29,7 @@ install_requires =
pandas>=0.19
tables>=3.2.1
nistats>=0.0.1b0
pybids>=0.9.4
pybids @ git+https://github.com/bids-standard/pybids.git@4cdcb0d
jinja2

[options.extras_require]
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0