<filename>examples/plot_neurosynth_implementation.py
# -*- coding: utf-8 -*-
r"""
NeuroLang Example based Implementing a NeuroSynth Query
====================================================

"""

# %%
import warnings

warnings.filterwarnings("ignore")

from pathlib import Path
from typing import Iterable

import nibabel
import nilearn.datasets
import nilearn.image
import nilearn.plotting
import numpy as np
import pandas as pd
from neurolang import ExplicitVBROverlay, NeurolangPDL
from neurolang.frontend.neurosynth_utils import get_ns_mni_peaks_reported

###############################################################################
# Data preparation
# ----------------

data_dir = Path.home() / "neurolang_data"

###############################################################################
# Load the MNI atlas and resample it to 4mm voxels

mni_t1 = nibabel.load(
    nilearn.datasets.fetch_icbm152_2009(data_dir=str(data_dir / "icbm"))["t1"]
)
mni_t1_4mm = nilearn.image.resample_img(mni_t1, np.eye(3) * 4)

###############################################################################
# Probabilistic Logic Programming in NeuroLang
# --------------------------------------------

nl = NeurolangPDL()


###############################################################################
# Adding new aggregation function to build a region overlay


@nl.add_symbol
def agg_create_region_overlay(
    i: Iterable, j: Iterable, k: Iterable, p: Iterable
) -> ExplicitVBROverlay:
    mni_coords = np.c_[i, j, k]
    return ExplicitVBROverlay(
        mni_coords, mni_t1_4mm.affine, p, image_dim=mni_t1_4mm.shape
    )


###############################################################################
# Load the NeuroSynth database

peak_data = get_ns_mni_peaks_reported(data_dir)
ijk_positions = np.round(
    nibabel.affines.apply_affine(
        np.linalg.inv(mni_t1_4mm.affine),
        peak_data[["x", "y", "z"]].values.astype(float),
    )
).astype(int)
peak_data["i"] = ijk_positions[:, 0]
peak_data["j"] = ijk_positions[:, 1]
peak_data["k"] = ijk_positions[:, 2]
peak_data = peak_data[["i", "j", "k", "id"]]

nl.add_tuple_set(peak_data, name="PeakReported")
study_ids = nl.load_neurosynth_study_ids(data_dir, "Study")
nl.add_uniform_probabilistic_choice_over_set(
    study_ids.value, name="SelectedStudy"
)
nl.load_neurosynth_term_study_associations(
    data_dir, "TermInStudyTFIDF", tfidf_threshold=1e-3
)


# %%
###############################################################################
# Probabilistic program and querying

with nl.scope as e:
    e.Activation[e.i, e.j, e.k] = e.PeakReported(
        e.i, e.j, e.k, e.s
    ) & e.SelectedStudy(e.s)
    e.TermAssociation[e.t] = e.SelectedStudy(e.s) & e.TermInStudyTFIDF(
        e.s, e.t, ...
    )
    e.ActivationGivenTerm[e.i, e.j, e.k, e.PROB[e.i, e.j, e.k]] = e.Activation(
        e.i, e.j, e.k
    ) // e.TermAssociation("auditory")
    e.ActivationGivenTermImage[
        agg_create_region_overlay(e.i, e.j, e.k, e.p)
    ] = e.ActivationGivenTerm(e.i, e.j, e.k, e.p)

    img_query = nl.query((e.x,), e.ActivationGivenTermImage(e.x))


# %%
###############################################################################
# Plotting results
# --------------------------------------------

result_image = img_query.fetch_one()[0].spatial_image()
img = result_image.get_fdata()
plot = nilearn.plotting.plot_stat_map(
    result_image, threshold=np.percentile(img[img > 0], 95)
)
nilearn.plotting.show()

<filename>examples/plot_neurosynth_implementation.py
# -*- coding: utf-8 -*-
r"""
NeuroLang Example based Implementing a NeuroSynth Query
====================================================

"""

# %%
import warnings

warnings.filterwarnings("ignore")

from pathlib import Path
from typing import Iterable

import nibabel
import nilearn.datasets
import nilearn.image
import nilearn.plotting
import numpy as np
import pandas as pd
from neurolang import ExplicitVBROverlay, NeurolangPDL
from neurolang.frontend.neurosynth_utils import get_ns_mni_peaks_reported

###############################################################################
# Data preparation
# ----------------

data_dir = Path.home() / "neurolang_data"

###############################################################################
# Load the MNI atlas and resample it to 4mm voxels

mni_t1 = nibabel.load(
    nilearn.datasets.fetch_icbm152_2009(data_dir=str(data_dir / "icbm"))["t1"]
)
mni_t1_4mm = nilearn.image.resample_img(mni_t1, np.eye(3) * 4)

###############################################################################
# Probabilistic Logic Programming in NeuroLang
# --------------------------------------------

nl = NeurolangPDL()


###############################################################################
# Adding new aggregation function to build a region overlay


@nl.add_symbol
def agg_create_region_overlay(
    i: Iterable, j: Iterable, k: Iterable, p: Iterable
) -> ExplicitVBROverlay:
    mni_coords = np.c_[i, j, k]
    return ExplicitVBROverlay(
        mni_coords, mni_t1_4mm.affine, p, image_dim=mni_t1_4mm.shape
    )


###############################################################################
# Load the NeuroSynth database

peak_data = get_ns_mni_peaks_reported(data_dir)
ijk_positions = np.round(
    nibabel.affines.apply_affine(
        np.linalg.inv(mni_t1_4mm.affine),
        peak_data[["x", "y", "z"]].values.astype(float),
    )
).astype(int)
peak_data["i"] = ijk_positions[:, 0]
peak_data["j"] = ijk_positions[:, 1]
peak_data["k"] = ijk_positions[:, 2]
peak_data = peak_data[["i", "j", "k", "id"]]

nl.add_tuple_set(peak_data, name="PeakReported")
study_ids = nl.load_neurosynth_study_ids(data_dir, "Study")
nl.add_uniform_probabilistic_choice_over_set(
    study_ids.value, name="SelectedStudy"
)
nl.load_neurosynth_term_study_associations(
    data_dir, "TermInStudyTFIDF", tfidf_threshold=1e-3
)


# %%
###############################################################################
# Probabilistic program and querying

with nl.scope as e:
    e.Activation[e.i, e.j, e.k] = e.PeakReported(
        e.i, e.j, e.k, e.s
    ) & e.SelectedStudy(e.s)
    e.TermAssociation[e.t] = e.SelectedStudy(e.s) & e.TermInStudyTFIDF(
        e.s, e.t, ...
    )
    e.ActivationGivenTerm[e.i, e.j, e.k, e.PROB[e.i, e.j, e.k]] = e.Activation(
        e.i, e.j, e.k
    ) // e.TermAssociation("auditory")
    e.ActivationGivenTermImage[
        agg_create_region_overlay(e.i, e.j, e.k, e.p)
    ] = e.ActivationGivenTerm(e.i, e.j, e.k, e.p)

    img_query = nl.query((e.x,), e.ActivationGivenTermImage(e.x))


# %%
###############################################################################
# Plotting results
# --------------------------------------------

result_image = img_query.fetch_one()[0].spatial_image()
img = result_image.get_fdata()
plot = nilearn.plotting.plot_stat_map(
    result_image, threshold=np.percentile(img[img > 0], 95)
)
nilearn.plotting.show()

# -*- coding: utf-8 -*- NeuroLang Example based Implementing a NeuroSynth Query ==================================================== # %% ############################################################################### # Data preparation # ---------------- ############################################################################### # Load the MNI atlas and resample it to 4mm voxels ############################################################################### # Probabilistic Logic Programming in NeuroLang # -------------------------------------------- ############################################################################### # Adding new aggregation function to build a region overlay ############################################################################### # Load the NeuroSynth database # %% ############################################################################### # Probabilistic program and querying # %% ############################################################################### # Plotting results # --------------------------------------------