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Fix the two sided test on IBMA Fishers and Stouffers estimators #903

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Fix the two sided test on IBMA Fishers and Stouffers estimators #903

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f1c7c4b
Fix the two sided test on IBMA Fishers and Stouffers estimators
JulioAPeraza Sep 10, 2024
f8a8e87
Upgrade upload-artifact to v4
JulioAPeraza Sep 10, 2024
43e5c31
Update testing.yml
JulioAPeraza Sep 10, 2024
69cc4d2
Update 12_plot_ibma_workflow.py
JulioAPeraza Sep 10, 2024
68c4425
Update testing.yml
JulioAPeraza Sep 10, 2024
e072d4a
Update ibma.py
JulioAPeraza Sep 10, 2024
23865c5
Update ibma.py
JulioAPeraza Sep 10, 2024
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126 changes: 67 additions & 59 deletions .github/workflows/testing.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ on:
- "main"
pull_request:
branches:
- '*'
- "*"

concurrency:
group: testing-${{ github.ref }}
Expand All @@ -26,37 +26,37 @@ jobs:
- id: result_step
uses: mstachniuk/ci-skip@master
with:
commit-filter: '[skip ci];[ci skip];[skip github]'
commit-filter-separator: ';'
commit-filter: "[skip ci];[ci skip];[skip github]"
commit-filter-separator: ";"

run_unit_tests:
name: Unit tests
needs: check_skip
if: ${{ needs.check_skip.outputs.skip == 'false' }}
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: ["ubuntu-latest", "macos-latest"]
python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
fail-fast: false
matrix:
os: ["ubuntu-latest", "macos-latest"]
python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]

defaults:
run:
shell: bash
steps:
- uses: actions/checkout@v2
- name: 'Set up python'
- name: "Set up python"
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: 'Install NiMARE'
python-version: ${{ matrix.python-version }}
- name: "Install NiMARE"
shell: bash {0}
run: pip install -e .[tests,cbmr]
- name: 'Run tests'
- name: "Run tests"
shell: bash {0}
run: make unittest
- name: Upload artifacts
uses: actions/upload-artifact@v2
uses: actions/upload-artifact@v4
with:
name: unit_${{ matrix.os }}_${{ matrix.python-version }}
path: coverage.xml
Expand All @@ -68,27 +68,27 @@ jobs:
if: ${{ needs.check_skip.outputs.skip == 'false' }}
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: ["ubuntu-latest"]
python-version: ["3.8"]
fail-fast: false
matrix:
os: ["ubuntu-latest"]
python-version: ["3.8"]
defaults:
run:
shell: bash
steps:
- uses: actions/checkout@v2
- name: 'Set up python'
- name: "Set up python"
uses: actions/setup-python@v2
with:
python-version: 3.8
- name: 'Install NiMARE'
python-version: 3.8
- name: "Install NiMARE"
shell: bash {0}
run: pip install -e .[minimum,tests,cbmr]
- name: 'Run tests'
- name: "Run tests"
shell: bash {0}
run: make unittest
- name: Upload artifacts
uses: actions/upload-artifact@v2
uses: actions/upload-artifact@v4
with:
name: unit_minimum
path: coverage.xml
Expand All @@ -100,27 +100,27 @@ jobs:
if: ${{ needs.check_skip.outputs.skip == 'false' }}
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: ["ubuntu-latest"]
python-version: ["3.8"]
fail-fast: false
matrix:
os: ["ubuntu-latest"]
python-version: ["3.8"]
defaults:
run:
shell: bash
steps:
- uses: actions/checkout@v2
- name: 'Set up python'
- name: "Set up python"
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: 'Install NiMARE'
python-version: ${{ matrix.python-version }}
- name: "Install NiMARE"
shell: bash {0}
run: pip install -e .[tests,cbmr]
- name: 'Run tests'
- name: "Run tests"
shell: bash {0}
run: make test_performance_estimators
- name: Upload artifacts
uses: actions/upload-artifact@v2
uses: actions/upload-artifact@v4
with:
name: performance_estimator
path: coverage.xml
Expand All @@ -132,27 +132,27 @@ jobs:
if: ${{ needs.check_skip.outputs.skip == 'false' }}
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: ["ubuntu-latest"]
python-version: ["3.8"]
fail-fast: false
matrix:
os: ["ubuntu-latest"]
python-version: ["3.8"]
defaults:
run:
shell: bash
steps:
- uses: actions/checkout@v2
- name: 'Set up python'
- name: "Set up python"
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: 'Install NiMARE'
python-version: ${{ matrix.python-version }}
- name: "Install NiMARE"
shell: bash {0}
run: pip install -e .[tests,cbmr]
- name: 'Run tests'
- name: "Run tests"
shell: bash {0}
run: make test_performance_correctors
- name: Upload artifacts
uses: actions/upload-artifact@v2
uses: actions/upload-artifact@v4
with:
name: performance_corrector
path: coverage.xml
Expand All @@ -164,27 +164,27 @@ jobs:
if: ${{ needs.check_skip.outputs.skip == 'false' }}
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: ["ubuntu-latest"]
python-version: ["3.8"]
fail-fast: false
matrix:
os: ["ubuntu-latest"]
python-version: ["3.8"]
defaults:
run:
shell: bash
steps:
- uses: actions/checkout@v2
- name: 'Set up python'
- name: "Set up python"
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: 'Install NiMARE'
python-version: ${{ matrix.python-version }}
- name: "Install NiMARE"
shell: bash {0}
run: pip install -e .[tests,cbmr]
- name: 'Run tests'
- name: "Run tests"
shell: bash {0}
run: make test_performance_smoke
- name: Upload artifacts
uses: actions/upload-artifact@v2
uses: actions/upload-artifact@v4
with:
name: performance_smoke
path: coverage.xml
Expand All @@ -196,41 +196,49 @@ jobs:
if: ${{ needs.check_skip.outputs.skip == 'false' }}
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: ["ubuntu-latest"]
python-version: ["3.8"]
fail-fast: false
matrix:
os: ["ubuntu-latest"]
python-version: ["3.8"]
defaults:
run:
shell: bash
steps:
- uses: actions/checkout@v2
- name: 'Set up python'
- name: "Set up python"
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: 'Install NiMARE'
python-version: ${{ matrix.python-version }}
- name: "Install NiMARE"
shell: bash {0}
run: pip install -e .[tests]
- name: 'Run tests'
- name: "Run tests"
shell: bash {0}
run: make test_cbmr_importerror
- name: Upload artifacts
uses: actions/upload-artifact@v2
uses: actions/upload-artifact@v4
with:
name: cbmr_importerror
path: coverage.xml
if: success()

upload_to_codecov:
name: Upload coverage
needs: [run_unit_tests,run_unit_tests_with_minimum_dependencies,test_performance_estimators,test_performance_correctors,test_performance_smoke,test_cbmr_importerror]
needs:
[
run_unit_tests,
run_unit_tests_with_minimum_dependencies,
test_performance_estimators,
test_performance_correctors,
test_performance_smoke,
test_cbmr_importerror,
]
runs-on: "ubuntu-latest"
steps:
- name: Checkout
uses: actions/checkout@v2
- name: Download artifacts
uses: actions/download-artifact@v2
uses: actions/download-artifact@v4
- name: Upload to CodeCov
uses: codecov/codecov-action@v4
with:
Expand Down
2 changes: 1 addition & 1 deletion examples/02_meta-analyses/12_plot_ibma_workflow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -78,7 +78,7 @@
###############################################################################
# Contribution table
# ``````````````````````````````````````````````````````````````````````````````
result.tables["z_corr-FDR_method-indep_diag-Jackknife_tab-counts_tail-positive"]
result.tables["z_corr-FDR_method-indep_diag-Jackknife_tab-counts"]

###############################################################################
# Report
Expand Down
65 changes: 50 additions & 15 deletions nimare/meta/ibma.py
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Original file line number Diff line number Diff line change
Expand Up @@ -228,7 +228,6 @@ class Fishers(IBMAEstimator):
def __init__(self, two_sided=True, **kwargs):
super().__init__(**kwargs)
self.two_sided = two_sided
self._mode = "concordant" if self.two_sided else "directed"

def _generate_description(self):
description = (
Expand All @@ -243,13 +242,32 @@ def _fit_model(self, stat_maps):
"""Fit the model to the data."""
n_studies, n_voxels = stat_maps.shape

pymare_dset = pymare.Dataset(y=stat_maps)
est = pymare.estimators.FisherCombinationTest(mode=self._mode)
est.fit_dataset(pymare_dset)
est_summary = est.summary()
# Run Stouffers for right tail
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suggestion (performance): Consider performance implications of running two separate tests for two-sided cases

The new implementation runs two separate tests when two_sided is True, which could potentially double the computation time. Consider if there's a way to optimize this, especially for large datasets.

pos_est = pymare.estimators.FisherCombinationTest(mode="directed")
pos_pymare_dset = pymare.Dataset(y=stat_maps)
pos_est.fit_dataset(pos_pymare_dset)
pos_est_summary = pos_est.summary()

z_map = pos_est_summary.z.squeeze()
p_map = pos_est_summary.p.squeeze()

if self.two_sided:
# Run Stouffers for left tail
neg_est = pymare.estimators.FisherCombinationTest(mode="directed")
neg_pymare_dset = pymare.Dataset(y=-stat_maps)
neg_est.fit_dataset(neg_pymare_dset)
neg_est_summary = neg_est.summary()

# Find the minimum p-values
p_map = np.minimum(p_map, neg_est_summary.p.squeeze())

# Create z_map based on which p-value is smaller
z_map = np.where(
p_map <= neg_est_summary.p.squeeze(),
z_map,
-neg_est_summary.z.squeeze(),
)

z_map = est_summary.z.squeeze()
p_map = est_summary.p.squeeze()
dof_map = np.tile(n_studies - 1, n_voxels).astype(np.int32)

return z_map, p_map, dof_map
Expand Down Expand Up @@ -381,7 +399,6 @@ def __init__(
self.normalize_contrast_weights = normalize_contrast_weights

self.two_sided = two_sided
self._mode = "concordant" if self.two_sided else "directed"

def _preprocess_input(self, dataset):
"""Preprocess additional inputs to the Estimator from the Dataset as needed."""
Expand Down Expand Up @@ -440,8 +457,6 @@ def _fit_model(self, stat_maps, study_mask=None, corr=None):
# when using the aggressive mask.
study_mask = np.arange(n_studies)

est = pymare.estimators.StoufferCombinationTest(mode=self._mode)

contrast_maps, sub_corr = None, None
if corr is not None:
contrast_maps = np.tile(self.inputs_["contrast_names"][study_mask], (n_voxels, 1)).T
Expand All @@ -460,12 +475,32 @@ def _fit_model(self, stat_maps, study_mask=None, corr=None):

weight_maps = np.tile(weights, (n_voxels, 1)).T

pymare_dset = pymare.Dataset(y=stat_maps, n=weight_maps, v=contrast_maps)
est.fit_dataset(pymare_dset, corr=sub_corr)
est_summary = est.summary()
# Run Stouffers for right tail
pos_est = pymare.estimators.StoufferCombinationTest(mode="directed")
pos_pymare_dset = pymare.Dataset(y=stat_maps, n=weight_maps, v=contrast_maps)
pos_est.fit_dataset(pos_pymare_dset, corr=sub_corr)
pos_est_summary = pos_est.summary()

z_map = pos_est_summary.z.squeeze()
p_map = pos_est_summary.p.squeeze()

if self.two_sided:
# Run Stouffers for left tail
neg_est = pymare.estimators.StoufferCombinationTest(mode="directed")
neg_pymare_dset = pymare.Dataset(y=-stat_maps, n=weight_maps, v=contrast_maps)
neg_est.fit_dataset(neg_pymare_dset, corr=sub_corr)
neg_est_summary = neg_est.summary()

# Find the minimum p-values
p_map = np.minimum(p_map, neg_est_summary.p.squeeze())

# Create z_map based on which p-value is smaller
z_map = np.where(
p_map <= neg_est_summary.p.squeeze(),
z_map,
-neg_est_summary.z.squeeze(),
)

z_map = est_summary.z.squeeze()
p_map = est_summary.p.squeeze()
dof_map = np.tile(n_studies - 1, n_voxels).astype(np.int32)

return z_map, p_map, dof_map
Expand Down
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