indi-net-extract 0.1.0.dev0__py3-none-any.whl

indi_net_extract-0.1.0.dev0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: indi-net-extract
+Version: 0.1.0.dev0
+Summary: Template-guided individual network extraction and spatial overlap evaluation
+License-Expression: BSD-3-Clause
+Project-URL: Source, https://github.com/sonia1maslova/indi-net-extract
+Project-URL: Documentation, https://github.com/sonia1maslova/indi-net-extract/blob/main/README.md
+Project-URL: Issues, https://github.com/sonia1maslova/indi-net-extract/issues
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: THIRD_PARTY_NOTICES.md
+Requires-Dist: numpy>=1.26
+Requires-Dist: scipy>=1.11
+Requires-Dist: nibabel>=5.2
+Requires-Dist: threadpoolctl>=3.1
+Dynamic: license-file
+
+# IndiNetExtract
+
+Python分发名（安装名）：`indi-net-extract`。Python导入名和源码包目录：`indinetextract`。
+
+模板引导的个体网络提取工具包，开发初版 `0.1.0.dev0`。目前提供Python源码，尚未发布到PyPI。
+
+输入被试ID列表、逐项对应的静息态影像路径，以及全体共用的模板和mask。输出每名被试的连续网络图、时间序列及运行记录。支持经典双回归β和独立NumPy/SciPy GIG-ICA。
+
+**每名被试只输入一份已经准备好的4D NIfTI。** 数据清洗、扫描标准化、拼接和空间配准在包外完成。批处理列表表示不同被试，不表示要拼接的扫描。算法内部所需的中心化、白化和双回归时间序列归一化仍保留。
+
+## 从源码安装
+
+当前为开发初版，尚未发布到PyPI。可从本仓库安装：
+
+```bash
+git clone https://github.com/sonia1maslova/indi-net-extract.git
+cd indi-net-extract
+python -m pip install .
+```
+
+## 快速使用
+
+在已具备NumPy、SciPy、NiBabel、threadpoolctl的环境中，将本包 `src` 加入 `PYTHONPATH`，或安装本地构建产物。已测试的软件版本和验证边界见 `docs/validation.md`；以下示例不下载或修改数据。
+
+安装已下载的wheel时，文件名中的分发名按打包规则写成 `indi_net_extract`：
+
+```bash
+python -m pip install /path/to/indi_net_extract-0.1.0.dev0-py3-none-any.whl
+```
+
+安装后仍使用 `from indinetextract import ...`。分发名中的连字符不用于Python导入语句。
+
+```python
+from indinetextract import extract_batch
+
+def main():
+    batch = extract_batch(
+        subject_ids=["sub-001", "sub-002"],
+        fmri_paths=[
+            "/data/sub-001/rest_preprocessed.nii.gz",
+            "/data/sub-002/rest_preprocessed.nii.gz",
+        ],
+        templates="/data/templates.nii.gz",
+        mask="/data/analysis_mask.nii.gz",
+        output_root="/results/gig_ica",
+        method="gig_ica",
+        n_jobs=2,
+        n_threads=2,
+    )
+    print(batch.summary)
+
+if __name__ == "__main__":
+    main()
+```
+
+并行采用独立进程，脚本需要上面的 `__main__` 保护。只处理一名时，也传入长度为1的两个列表。输入文件名不必含被试ID；包按列表位置配对，不推测文件属于谁。
+
+| 参数 | 含义 |
+| --- | --- |
+| `subject_ids` | 非空且唯一的字符串ID列表 |
+| `fmri_paths` | 等长路径列表，每条路径是一名被试的一份4D影像 |
+| `templates` | 同一份4D空间模板，第四维为K个成分 |
+| `mask` | 同一份3D二值分析mask |
+| `method` | `"dual_regression"` 或 `"gig_ica"` |
+| `n_jobs=1` | 最多同时处理的被试数，即进程数 |
+| `n_threads=2` | 每名被试数值计算的线程预算 |
+| `label="extraction"` | 被试目录下的本次输出标签；可用不同标签区分方法、模板或测量日 |
+| `on_error="continue"` | 记录失败后继续；`"raise"` 表示停止提交新被试，等待正在运行的被试结束后报错 |
+| `work_dir=None` | 可选临时存储目录；每名被试使用独立临时子目录 |
+
+例如 `n_jobs=3, n_threads=2` 表示最多3名被试同时拟合，每名的数值运算预算为2线程。它不保证总内存足够；GIG-ICA仍需白化和SVD工作内存。默认串行执行，不自动增加进程。
+
+## 输出
+
+```text
+output_root/
+  _batches/<batch_id>/
+    inputs.tsv                   # 保存原ID—影像配对
+    summary.tsv                  # 顺序与输入一致，包含状态及失败原因
+    metadata.json                # 共用设置、环境及源码指纹
+  sub-001/extraction/
+    continuous_components.nii.gz  # X×Y×Z×K，连续成分
+    timecourses.tsv              # T×K，行是时间点，无标题行
+    components.tsv               # 0起始图像索引与成分ID
+    mask.nii.gz
+    metadata.json
+  sub-002/extraction/
+    ...
+```
+
+连续图的第四维是**成分**，不是时间；第i张图对应第i个模板。默认成分ID为C1…CK。双回归输出空间β，GIG-ICA输出成分权重，两者不当作统计Z或概率。
+
+一名完成后立即保存。`BatchResult`只返回轻量记录和文件路径，不把全体影像留在内存。失败被试不产生一个伪成功的结果目录。默认不覆盖已有结果；显式调用结果对象的 `save(overwrite=True)` 时，旧目录改名为备份并保留。
+
+## 独立后处理与模板Dice
+
+已经提取好的连续图可以重新载入，改变平滑或Top-N时不用重新拟合：
+
+```python
+from indinetextract import NetworkResult, postprocess_maps, template_dice, overlap_fraction
+
+fit = NetworkResult.load("/results/gig_ica/sub-001/extraction")
+binary = postprocess_maps(
+    fit,
+    fwhm_mm=6,
+    count_reference="/data/fixed_binary_reference.nii.gz",
+)
+binary.save("/results/gig_ica", label="fwhm_6mm")
+
+dice = template_dice(binary, reference="/data/fixed_binary_reference.nii.gz")
+print(dice.per_component, dice.mean_dice)
+dice.save("/results/gig_ica", label="fwhm_6mm/template_dice")
+
+pleiotropy = overlap_fraction(binary)  # 3D NIfTI对象，值为所选成分比例
+```
+
+- `count_reference`必须是二值图，在mask内计数得到每成分N。也可以改用显式的 `top_n=[...]`，两者必须二选一。
+- 用于提取的模板允许连续值；用于计数和Dice的参考图必须明确为0/1。切换提取模板不自动改变N。
+- 平滑使用 `G(M*f)/G(M)`，仅沿空间维，保留原mask。每个宽度都从原始连续图开始。NIfTI空间单位unknown时按mm解释并记录；正宽度平滑拒绝剪切网格。
+- Top-N按有限的有符号数值降序选严格N个，允许零值和负值；并列按原始Fortran体素索引。候选不足时报错，不自动缩小N。
+- Dice矩阵行是个体成分，列是参考成分；对应分数是对角线。不自动换序、翻符号或选择最佳配对。
+- 单侧为空时Dice为0，双侧为空为NaN；存在无效对应成分时完整K成分均值为NaN。JSON中缺失数值保存为null，TSV中为nan。
+- `overlap_fraction`为K张二值图的逐体素平均；它不自动构成统计显著性检验。
+
+## 输入约束与验证边界
+
+所有影像必须事先对齐，空间形状一致，affine数值在记录的容差内一致。mask显式提供，保持不变。mask外不参与计算；mask内NaN/Inf或时间常量BOLD序列会报错，包不自动插补或删除体素。
+
+独立Python GIG核心保留原算法源码许可与控制流程。此前合成数据及三名真实被试有MATLAB对照，真实数据不是所有数值严格相等。此包封装的验证范围和具体检查见 [docs/validation.md](docs/validation.md)；不能只依据模板Dice较高就判定个体网络科学有效。
+
+当前实际验证使用Python3.13项目环境；其他Python版本和Windows原生并行尚需分别测试。声明最低Python版本不等于所有组合均已测试。
+
+自动单元测试不依赖MATLAB或FSL；本轮另外完成了两种模板的小型FSL对照。更新算法一致性结论时，应保留输入、源码、参数和数值误差。
+
+## 来源与许可
+
+GIG数值核心位于 `_algorithms/gig_ica.py`，来自已有NumPy/SciPy移植；原始来源为GIFT `icatb_gigicar.m`，作者Yuhui Du、Yong Fan。版权与许可保留在文件头及 [THIRD_PARTY_NOTICES.md](THIRD_PARTY_NOTICES.md)。其他初版代码采用BSD-3-Clause许可。

indi_net_extract-0.1.0.dev0.dist-info/RECORD

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+indi_net_extract-0.1.0.dev0.dist-info/RECORD,,

indi_net_extract-0.1.0.dev0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: setuptools (83.0.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

indi_net_extract-0.1.0.dev0.dist-info/licenses/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2026, indinetextract contributors
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+3. Neither the name of the copyright holder nor the names of its contributors
+   may be used to endorse or promote products derived from this software
+   without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+The GIG-ICA source additionally retains its original notice; see
+THIRD_PARTY_NOTICES.md and src/indinetextract/_algorithms/gig_ica.py.

indi_net_extract-0.1.0.dev0.dist-info/licenses/THIRD_PARTY_NOTICES.md

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+# Third-party source notices
+
+The GIG-ICA Python core retains the following original notice. Original source: GIFT icatb_gigicar.m; source SHA256: 6a0bbf665524d0122686ce6416d06350cb21d71f90460c282aa539f76803773c.
+
+Copyright (c) 2012 Yuhui DU and Yong FAN
+All rights reserved.
+
+Redistribution and use in source or any other forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice,
+  this list of conditions and the following disclaimer.
+* Redistributions in any other form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+* Neither the names of the copyright holders nor the names of future
+  contributors may be used to endorse or promote products derived from this
+  software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.

indi_net_extract-0.1.0.dev0.dist-info/top_level.txt

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+indinetextract

indinetextract/__init__.py

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+"""Template-guided extraction from already prepared resting-state fMRI."""
+from ._version import __version__
+from ._types import (BatchExecutionError, BatchResult, BinaryMapsResult,
+                     DiceResult, NetworkResult)
+from .batch import extract_batch
+from .postprocessing import postprocess_maps
+from .evaluation import overlap_fraction, template_dice
+
+__all__ = [
+    "extract_batch", "postprocess_maps", "template_dice", "overlap_fraction",
+    "NetworkResult", "BinaryMapsResult", "DiceResult", "BatchResult",
+    "BatchExecutionError", "__version__",
+]

indinetextract/_algorithms/__init__.py

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+"""Private numerical implementations with explicit source provenance."""

indinetextract/_algorithms/dual_regression.py

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+"""Minimal classic dual regression, following the project's stock-FSL check.
+
+The stage-one template normalization, accumulated cross-products, SVD-based
+inverse Gram, stage-two intercept and normal-equation solver are adapted from
+``dr_improvements_20261031/dr_core.py``. The selected route is exactly the
+``official_compatible_fit`` convention in ``validate_fsl_dr.py``: one input,
+``run_baselines=False``, ``temporal_ddof=1`` (FSL ``des_norm=1``).
+
+Only continuous stage-two beta maps and normalized timecourses are calculated.
+The module adds no spatial prior, frame weighting or statistical-Z output.
+Caller-side validation must reject nonfinite or constant masked observations;
+this implementation never discards a voxel or changes the analysis support.
+"""
+from __future__ import annotations
+
+import time
+
+import numpy as np
+
+
+SOURCE_NAME = "dr_improvements_20261031/dr_core.py"
+SOURCE_SHA256 = "24b366a5e8420b8ecc01f1dca59fe35c8d37f816c3ce53e204ed20e75ffd9052"
+VALIDATOR_NAME = "rest_factorial_pilot/validate_fsl_dr.py"
+VALIDATOR_SHA256 = "0da89b814179a215e085cc81648f77b688d37fa2d41028ea523dd3e2d2dbe15c"
+
+
+def rank_info(matrix, name):
+    """Use the source core's float64 SVD tolerance and full-column-rank rule."""
+    singular = np.linalg.svd(matrix, compute_uv=False)
+    tolerance = np.finfo(np.float64).eps * max(matrix.shape) * singular[0]
+    rank = int(np.count_nonzero(singular > tolerance))
+    if rank != matrix.shape[1]:
+        raise ValueError(
+            "%s is rank deficient: rank %d, %d columns"
+            % (name, rank, matrix.shape[1])
+        )
+    return {
+        "rank": rank,
+        "condition_number": float(singular[0] / singular[-1]),
+        "singular_values": singular.tolist(),
+        "rank_tolerance": float(tolerance),
+    }
+
+
+def fit_dual_regression(data, reference, *, chunk_size=8192):
+    """Fit float64 classic beta maps from Y[time, voxel], S[voxel, component].
+
+    There is one complete, already prepared fMRI input. Temporal demeaning
+    here is an intrinsic regression operation; there is no input variance
+    normalization, run partitioning or concatenation.
+    """
+    started = time.perf_counter()
+    if np.iscomplexobj(data) or np.iscomplexobj(reference):
+        raise ValueError("Data and templates must be real-valued")
+    data = np.asarray(data)
+    reference = np.asarray(reference, dtype=np.float64)
+    if data.ndim != 2 or reference.ndim != 2:
+        raise ValueError("Expected data [time, voxel] and reference [voxel, component]")
+    n_timepoints, n_voxels = data.shape
+    n_components = reference.shape[1]
+    if reference.shape[0] != n_voxels or n_components < 1:
+        raise ValueError("Data and reference have incompatible dimensions")
+    if n_voxels <= n_components:
+        raise ValueError("Insufficient masked voxels for the spatial template design")
+    if n_timepoints <= n_components + 1:
+        raise ValueError("Insufficient timepoints for the stage-two timecourse design")
+    if (
+        isinstance(chunk_size, (bool, np.bool_))
+        or not isinstance(chunk_size, (int, np.integer))
+        or chunk_size < 1
+    ):
+        raise ValueError("chunk_size must be a positive integer")
+    if not np.isfinite(reference).all():
+        raise ValueError("Templates contain nonfinite values inside the analysis mask")
+
+    means = np.mean(reference, axis=0)
+    spatial_scales = np.std(reference, axis=0, ddof=0)
+    if np.any(spatial_scales <= 0) or not np.isfinite(spatial_scales).all():
+        raise ValueError("A template is spatially constant inside the analysis mask")
+    matrix = (reference - means) / spatial_scales
+    template_rank = rank_info(matrix, "Spatial template design")
+    left, singular, right = np.linalg.svd(matrix, full_matrices=False)
+    del left
+    gram_inverse = (right.T / (singular * singular)) @ right
+
+    cross = np.zeros((n_timepoints, n_components), dtype=np.float64)
+    for start in range(0, n_voxels, chunk_size):
+        stop = min(start + chunk_size, n_voxels)
+        block = np.array(data[:, start:stop], dtype=np.float64, copy=True)
+        if not np.isfinite(block).all():
+            raise ValueError("BOLD values are nonfinite inside the analysis mask")
+        block -= block.mean(axis=0, keepdims=True)
+        cross += block @ matrix[start:stop]
+    raw = cross @ gram_inverse
+    centered = raw - raw.mean(axis=0, keepdims=True)
+    temporal_scales = np.std(centered, axis=0, ddof=1)
+    if np.any(temporal_scales <= 0) or not np.isfinite(temporal_scales).all():
+        raise ValueError("A stage-one timecourse is constant or invalid")
+    timecourses = centered / temporal_scales
+    design = np.column_stack((np.ones(n_timepoints), timecourses))
+    timecourse_rank = rank_info(design, "Stage-two timecourse design")
+    linear = np.linalg.solve(design.T @ design, design.T)
+    components = np.empty((n_voxels, n_components), dtype=np.float64)
+    for start in range(0, n_voxels, chunk_size):
+        stop = min(start + chunk_size, n_voxels)
+        block = np.array(data[:, start:stop], dtype=np.float64, copy=True)
+        block -= block.mean(axis=0, keepdims=True)
+        components[start:stop] = (linear @ block)[1:].T
+    if not np.isfinite(components).all() or not np.isfinite(timecourses).all():
+        raise FloatingPointError("Classic dual regression produced nonfinite output")
+    return {
+        "components": components,
+        "timecourses": timecourses,
+        "metadata": {
+            "implementation": "classic_dual_regression_FSL_des_norm_1_convention",
+            "source_name": SOURCE_NAME,
+            "source_sha256": SOURCE_SHA256,
+            "validator_name": VALIDATOR_NAME,
+            "validator_sha256": VALIDATOR_SHA256,
+            "n_timepoints": n_timepoints,
+            "n_voxels": n_voxels,
+            "n_components": n_components,
+            "spatial_template_centering": True,
+            "spatial_template_standardization_ddof": 0,
+            "spatial_template_means": means.tolist(),
+            "spatial_template_sd": spatial_scales.tolist(),
+            "temporal_centering_Y": "whole_single_input_per_voxel",
+            "stage1_timecourse_centering": True,
+            "temporal_standardization_ddof": 1,
+            "stage1_timecourse_sd": temporal_scales.tolist(),
+            "timecourses_returned": "centered_sample_SD_normalized_stage1",
+            "stage2_intercept": True,
+            "n_nuisance": 1,
+            "run_baselines": False,
+            "des_norm": 1,
+            "template_rank_diagnostics": template_rank,
+            "timecourse_rank_diagnostics": timecourse_rank,
+            "residual_degrees_of_freedom": n_timepoints - n_components - 1,
+            "map_definition": "stage2_continuous_beta",
+            "output_dtype": "float64",
+            "source_beta_storage_dtype": "float32",
+            "spatial_prior_added": False,
+            "frame_weighting_added": False,
+            "fsl_invoked": False,
+            "fsl_equivalence_tested_for_this_code": False,
+            "elapsed_seconds": time.perf_counter() - started,
+        },
+    }