"""
ROI-based decoding analysis in Haxby et al. dataset
===================================================

In this script we reproduce the data analysis
conducted by :footcite:t:`Haxby2001`.

Specifically, we look at decoding accuracy for different objects in
three different masks: the full ventral stream (mask_vt), the house
selective areas (mask_house) and the face selective areas (mask_face),
that have been defined via a standard GLM-based analysis.

"""

# Fetch data using nilearn dataset fetcher
from nilearn import datasets
from nilearn.plotting import show

# %%
# Load and prepare the data
# -------------------------


# by default we fetch 2nd subject data for analysis
haxby_dataset = datasets.fetch_haxby()
func_filename = haxby_dataset.func[0]

# Print basic information on the dataset
print(
    "First subject anatomical nifti image (3D) located is "
    f"at: {haxby_dataset.anat[0]}"
)
print(
    f"First subject functional nifti image (4D) is located at: {func_filename}"
)

# load labels
import pandas as pd

# Load nilearn NiftiMasker, the practical masking and unmasking tool
from nilearn.maskers import NiftiMasker

labels = pd.read_csv(haxby_dataset.session_target[0], sep=" ")
stimuli = labels["labels"]
# identify resting state labels in order to be able to remove them
task_mask = stimuli != "rest"

# find names of remaining active labels
categories = stimuli[task_mask].unique()

# extract tags indicating to which acquisition run a tag belongs
run_labels = labels["chunks"][task_mask]

# apply the task_mask to  fMRI data (func_filename)
from nilearn.image import index_img

task_data = index_img(func_filename, task_mask)

# %%
# Decoding on the different masks
# -------------------------------
#
# The classifier used here is a support vector classifier (svc).
# We use
# :class:`~nilearn.decoding.Decoder` and specify the classifier.
import numpy as np

# Make a data splitting object for cross validation
from sklearn.model_selection import LeaveOneGroupOut

from nilearn.decoding import Decoder

cv = LeaveOneGroupOut()

# %%
# We use :class:`~nilearn.decoding.Decoder` to estimate a baseline.

import warnings

mask_names = ["mask_vt", "mask_face", "mask_house"]

mask_scores = {}
mask_chance_scores = {}

for mask_name in mask_names:
    print(f"Working on {mask_name}")
    # For decoding, standardizing is often very important
    mask_filename = haxby_dataset[mask_name][0]
    masker = NiftiMasker(mask_img=mask_filename, standardize="zscore_sample")
    mask_scores[mask_name] = {}
    mask_chance_scores[mask_name] = {}

    for category in categories:
        print(f"Processing {mask_name} {category}")
        classification_target = stimuli[task_mask] == category
        # Specify the classifier to the decoder object.
        # With the decoder we can input the masker directly.
        # We are using the svc_l1 here because it is intra subject.
        decoder = Decoder(
            estimator="svc_l1",
            cv=cv,
            mask=masker,
            scoring="roc_auc",
            standardize="zscore_sample",
        )

        with warnings.catch_warnings():
            # ignore warnings thrown because the ROI mask we are using
            # are much smaller than the whole brain.
            warnings.filterwarnings(action="ignore", category=UserWarning)
            decoder.fit(task_data, classification_target, groups=run_labels)

        mask_scores[mask_name][category] = decoder.cv_scores_[1]
        mean = np.mean(mask_scores[mask_name][category])
        std = np.std(mask_scores[mask_name][category])
        print(f"Scores: {mean:1.2f} +- {std:1.2f}")

        dummy_classifier = Decoder(
            estimator="dummy_classifier",
            cv=cv,
            mask=masker,
            scoring="roc_auc",
            standardize="zscore_sample",
        )

        with warnings.catch_warnings():
            # ignore warnings thrown because the ROI mask we are using
            # are much smaller than the whole brain.
            warnings.filterwarnings(action="ignore", category=UserWarning)
            dummy_classifier.fit(
                task_data, classification_target, groups=run_labels
            )

        mask_chance_scores[mask_name][category] = dummy_classifier.cv_scores_[
            1
        ]


# %%
# We make a simple bar plot to summarize the results
# --------------------------------------------------
import matplotlib.pyplot as plt

plt.figure(constrained_layout=True)

tick_position = np.arange(len(categories))
plt.xticks(tick_position, categories, rotation=45)

for color, mask_name in zip("rgb", mask_names):
    score_means = [
        np.mean(mask_scores[mask_name][category]) for category in categories
    ]
    plt.bar(
        tick_position, score_means, label=mask_name, width=0.25, color=color
    )

    score_chance = [
        np.mean(mask_chance_scores[mask_name][category])
        for category in categories
    ]
    plt.bar(
        tick_position,
        score_chance,
        width=0.25,
        edgecolor="k",
        facecolor="none",
    )

    tick_position = tick_position + 0.2

plt.ylabel("Classification accuracy (AUC score)")
plt.xlabel("Visual stimuli category")
plt.ylim(0.3, 1)
plt.legend(loc="lower right")
plt.title("Category-specific classification accuracy for different masks")

show()

# %%
# References
# ----------
#
# .. footbibliography::


# sphinx_gallery_dummy_images=1
