imc-histotools 0.1.0__tar.gz

imc_histotools-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Guojun Han Laboratory @PKU
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

imc_histotools-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: imc-histotools
+Version: 0.1.0
+Summary: Digital pathology analysis tools for the Selenium (Se) IMC paper: virtual IHC rendering, Qupath ROI annotation, and pixel-wise H-score classification.
+Author: Guojun Han Laboratory @PKU
+License: MIT
+Project-URL: Homepage, https://github.com/gjhan100/IMC-HistoTools
+Project-URL: Repository, https://github.com/gjhan100/IMC-HistoTools
+Project-URL: Issues, https://github.com/gjhan100/IMC-HistoTools/issues
+Keywords: IMC,imaging mass cytometry,digital pathology,virtual IHC,H-score,pixel-wise H-score,Qupath,geojson,selenium
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.20
+Requires-Dist: opencv-python>=4.5
+Requires-Dist: matplotlib>=3.4
+Requires-Dist: tifffile>=2021.0
+Dynamic: license-file
+
+<p align="center"><img src="https://raw.githubusercontent.com/gjhan100/IMC-HistoTools/main/assets/261013_Github.png" width="700"></p>
+
+[![Python Versions](https://img.shields.io/badge/python-3.8+-brightgreen.svg)](https://pypi.org/project/imc-histotools)
+[![PyPI](https://img.shields.io/pypi/v/imc-histotools.svg?color=brightgreen&style=flat)](https://pypi.org/project/imc-histotools)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+**IMC-HistoTools** is a digital-pathology toolkit that bridges **imaging mass cytometry (IMC)** and **histopathology**, developed for the Selenium (Se) IMC study. It turns raw IMC channels into brightfield-like virtual IHC images, quantifies marker expression as **pixel-wise H-scores** on Qupath annotations, and renders **virtual multiplex** images from consecutive sections.
+
+# Functionality
+
+| Function | Description |
+| --- | --- |
+| `virtual_IHC` | Synthesise an IHC / brightfield-like RGB image from IMC channels using the Beer–Lambert absorbance model (per-channel gamma, background threshold, stain colour bar). |
+| `virtual_IHC_ROI` | Same as above but zooms into a local region while **keeping the original pixel coordinates**. |
+| `virtual_IHC_annotation` | Rasterise Qupath `.geojson` polygon annotations into ROI boolean masks. |
+| `Hscore_threshold` | Build classification thresholds from reference ROIs (Negative / Low / Medium / High) using **mean / median / geometric-mean / all**. |
+| `pix_Hscore_map` | Classify every pixel into NP / LP / MP / HP, export a per-pixel CSV, and produce publication figures (classification map + bar chart & table). |
+
+# Install IMC-HistoTools
+
+### Using pip [![PyPI](https://img.shields.io/pypi/v/imc-histotools.svg?color=brightgreen&style=flat)](https://pypi.org/project/imc-histotools)
+```console
+pip install imc-histotools
+```
+
+### From GitHub [![GitHub](https://img.shields.io/badge/github-source-blue.svg)](https://github.com/gjhan100/IMC-HistoTools)
+```console
+git clone https://github.com/gjhan100/IMC-HistoTools.git
+cd IMC-HistoTools
+pip install -e .
+```
+
+# Usage
+
+<details>
+<summary><strong>1. Virtual IHC from IMC raw tiff</strong></summary>
+
+Render a brightfield-like IHC image from raw (or [0,1]-normalised) IMC channels.
+`Blue` is typically the nuclear marker (DNA); `Brown`/`Red` are membrane / lineage markers.
+
+```python
+import numpy as np
+import tifffile
+from IMC_HistoTools import virtual_IHC, virtual_IHC_ROI
+
+# read IMC channels
+dna = tifffile.imread("ROI_001_193Ir-DNA_cor.tiff").astype(np.float32)   # nuclear
+se  = tifffile.imread("ROI_001_Se-Ecadherin_cor.tiff").astype(np.float32) # membrane
+
+# full-image virtual IHC  (Blue = DNA, Brown = E-cadherin-Se)
+virtual_IHC(
+    Blue_image=dna, Red_image=None, Brown_image=se,
+    blue_name="DNA", brown_name="E-cadherin (Se)",
+    brown_threshold=0.1,          # background removal (< threshold -> 0)
+    brown_bar=True,               # show stain colour bar
+    save_dir="out/virtual_IHC.png",
+)
+
+# local region, keeping original pixel coordinates
+virtual_IHC_ROI(
+    Blue_image=dna, Red_image=None, Brown_image=se,
+    X0=2250, X1=3000, Y0=1250, Y1=2000, TICK=250,
+    save_dir="out/virtual_IHC_ROI.png",
+)
+```
+</details>
+
+<details>
+<summary><strong>2. Pixel-wise H-score with Qupath annotation</strong></summary>
+
+Load tissue-region and reference-ROI annotations exported from Qupath, calibrate the
+thresholds from the Negative / Low / Medium / High reference ROIs, then classify every
+pixel and export a CSV + figures.
+
+```python
+from IMC_HistoTools import virtual_IHC_annotation, Hscore_threshold, pix_Hscore_map
+
+marker = tifffile.imread("Normalize/ROI_001_Se_crop_normal.tiff").astype(np.float32)
+tissue = tifffile.imread("Mask/mask_crop.tiff") > 0
+
+# 1) tissue-region annotations (Normal mucosa / Tumor center / Invasive front / ...)
+ann = virtual_IHC_annotation(marker, "tissue_regions.geojson")
+
+# 2) reference ROIs (Negative / Low / Medium / High) for threshold calibration
+ref = virtual_IHC_annotation(marker, "reference_ROIs.geojson",
+                             region_order=["Negative", "Low", "Medium", "High"])
+
+# 3) thresholds from the reference ROIs  (stat: 'mean'/'median'/'geomean'/'all')
+thr = Hscore_threshold(
+    marker,
+    Np=ref["masks"]["Negative"], Lp=ref["masks"]["Low"],
+    Mp=ref["masks"]["Medium"],   Hp=ref["masks"]["High"],
+    tissue_mask=tissue, stat="median",
+)
+print(thr["thresholds"])          # (Lp, Mp, Hp)
+
+# 4) per-pixel H-score map + CSV + bar chart / table
+res = pix_Hscore_map(
+    marker,
+    Hscore_threshold_annotation=ref["masks"],   # Lp / Mp / Hp reference ROIs
+    tissue_annotation=ann["masks"],             # non-empty -> bar chart + table
+    tissue_mask=tissue,
+    stat="median",
+    delta=2, kernel=(5, 5),                     # Gaussian blur for the map display only
+    save_dir="out/",
+)
+res["csv_path"]        # per-pixel classification: x, y, intensity, score, category
+```
+
+Classification: `intensity < Lp` → 0 (NP), `[Lp, Mp)` → 1 (LP), `[Mp, Hp)` → 2 (MP),
+`>= Hp` → 3 (HP). The bar-chart statistics always use the **non-blurred** classification.
+</details>
+
+<details>
+<summary><strong>3. Virtual multiplexing from consecutive sections</strong></summary>
+
+Feed registered channels from consecutive sections into the three colour channels of
+`virtual_IHC` to obtain a single virtual-multiplex image (blue / red / brown).
+
+```python
+from IMC_HistoTools import virtual_IHC
+
+virtual_IHC(
+    Blue_image=dna,     # section A — DNA        (nuclear,    blue)
+    Red_image=cd45,     # section B — CD45       (red)
+    Brown_image=ecad,   # section C — E-cadherin (membrane,   brown)
+    blue_name="DNA", red_name="CD45", brown_name="E-cadherin",
+    blue_bar=True, red_bar=True, brown_bar=True,
+    save_dir="out/virtual_multiplex.png",
+)
+```
+</details>
+
+# Citation
+
+If you use **IMC-HistoTools** in your research, please cite the Se IMC paper (citation
+to be added upon publication).
+
+# License
+
+This project is licensed under the **MIT License** — see the [LICENSE](LICENSE) file.

imc_histotools-0.1.0/README.md

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+<p align="center"><img src="https://raw.githubusercontent.com/gjhan100/IMC-HistoTools/main/assets/261013_Github.png" width="700"></p>
+
+[![Python Versions](https://img.shields.io/badge/python-3.8+-brightgreen.svg)](https://pypi.org/project/imc-histotools)
+[![PyPI](https://img.shields.io/pypi/v/imc-histotools.svg?color=brightgreen&style=flat)](https://pypi.org/project/imc-histotools)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+**IMC-HistoTools** is a digital-pathology toolkit that bridges **imaging mass cytometry (IMC)** and **histopathology**, developed for the Selenium (Se) IMC study. It turns raw IMC channels into brightfield-like virtual IHC images, quantifies marker expression as **pixel-wise H-scores** on Qupath annotations, and renders **virtual multiplex** images from consecutive sections.
+
+# Functionality
+
+| Function | Description |
+| --- | --- |
+| `virtual_IHC` | Synthesise an IHC / brightfield-like RGB image from IMC channels using the Beer–Lambert absorbance model (per-channel gamma, background threshold, stain colour bar). |
+| `virtual_IHC_ROI` | Same as above but zooms into a local region while **keeping the original pixel coordinates**. |
+| `virtual_IHC_annotation` | Rasterise Qupath `.geojson` polygon annotations into ROI boolean masks. |
+| `Hscore_threshold` | Build classification thresholds from reference ROIs (Negative / Low / Medium / High) using **mean / median / geometric-mean / all**. |
+| `pix_Hscore_map` | Classify every pixel into NP / LP / MP / HP, export a per-pixel CSV, and produce publication figures (classification map + bar chart & table). |
+
+# Install IMC-HistoTools
+
+### Using pip [![PyPI](https://img.shields.io/pypi/v/imc-histotools.svg?color=brightgreen&style=flat)](https://pypi.org/project/imc-histotools)
+```console
+pip install imc-histotools
+```
+
+### From GitHub [![GitHub](https://img.shields.io/badge/github-source-blue.svg)](https://github.com/gjhan100/IMC-HistoTools)
+```console
+git clone https://github.com/gjhan100/IMC-HistoTools.git
+cd IMC-HistoTools
+pip install -e .
+```
+
+# Usage
+
+<details>
+<summary><strong>1. Virtual IHC from IMC raw tiff</strong></summary>
+
+Render a brightfield-like IHC image from raw (or [0,1]-normalised) IMC channels.
+`Blue` is typically the nuclear marker (DNA); `Brown`/`Red` are membrane / lineage markers.
+
+```python
+import numpy as np
+import tifffile
+from IMC_HistoTools import virtual_IHC, virtual_IHC_ROI
+
+# read IMC channels
+dna = tifffile.imread("ROI_001_193Ir-DNA_cor.tiff").astype(np.float32)   # nuclear
+se  = tifffile.imread("ROI_001_Se-Ecadherin_cor.tiff").astype(np.float32) # membrane
+
+# full-image virtual IHC  (Blue = DNA, Brown = E-cadherin-Se)
+virtual_IHC(
+    Blue_image=dna, Red_image=None, Brown_image=se,
+    blue_name="DNA", brown_name="E-cadherin (Se)",
+    brown_threshold=0.1,          # background removal (< threshold -> 0)
+    brown_bar=True,               # show stain colour bar
+    save_dir="out/virtual_IHC.png",
+)
+
+# local region, keeping original pixel coordinates
+virtual_IHC_ROI(
+    Blue_image=dna, Red_image=None, Brown_image=se,
+    X0=2250, X1=3000, Y0=1250, Y1=2000, TICK=250,
+    save_dir="out/virtual_IHC_ROI.png",
+)
+```
+</details>
+
+<details>
+<summary><strong>2. Pixel-wise H-score with Qupath annotation</strong></summary>
+
+Load tissue-region and reference-ROI annotations exported from Qupath, calibrate the
+thresholds from the Negative / Low / Medium / High reference ROIs, then classify every
+pixel and export a CSV + figures.
+
+```python
+from IMC_HistoTools import virtual_IHC_annotation, Hscore_threshold, pix_Hscore_map
+
+marker = tifffile.imread("Normalize/ROI_001_Se_crop_normal.tiff").astype(np.float32)
+tissue = tifffile.imread("Mask/mask_crop.tiff") > 0
+
+# 1) tissue-region annotations (Normal mucosa / Tumor center / Invasive front / ...)
+ann = virtual_IHC_annotation(marker, "tissue_regions.geojson")
+
+# 2) reference ROIs (Negative / Low / Medium / High) for threshold calibration
+ref = virtual_IHC_annotation(marker, "reference_ROIs.geojson",
+                             region_order=["Negative", "Low", "Medium", "High"])
+
+# 3) thresholds from the reference ROIs  (stat: 'mean'/'median'/'geomean'/'all')
+thr = Hscore_threshold(
+    marker,
+    Np=ref["masks"]["Negative"], Lp=ref["masks"]["Low"],
+    Mp=ref["masks"]["Medium"],   Hp=ref["masks"]["High"],
+    tissue_mask=tissue, stat="median",
+)
+print(thr["thresholds"])          # (Lp, Mp, Hp)
+
+# 4) per-pixel H-score map + CSV + bar chart / table
+res = pix_Hscore_map(
+    marker,
+    Hscore_threshold_annotation=ref["masks"],   # Lp / Mp / Hp reference ROIs
+    tissue_annotation=ann["masks"],             # non-empty -> bar chart + table
+    tissue_mask=tissue,
+    stat="median",
+    delta=2, kernel=(5, 5),                     # Gaussian blur for the map display only
+    save_dir="out/",
+)
+res["csv_path"]        # per-pixel classification: x, y, intensity, score, category
+```
+
+Classification: `intensity < Lp` → 0 (NP), `[Lp, Mp)` → 1 (LP), `[Mp, Hp)` → 2 (MP),
+`>= Hp` → 3 (HP). The bar-chart statistics always use the **non-blurred** classification.
+</details>
+
+<details>
+<summary><strong>3. Virtual multiplexing from consecutive sections</strong></summary>
+
+Feed registered channels from consecutive sections into the three colour channels of
+`virtual_IHC` to obtain a single virtual-multiplex image (blue / red / brown).
+
+```python
+from IMC_HistoTools import virtual_IHC
+
+virtual_IHC(
+    Blue_image=dna,     # section A — DNA        (nuclear,    blue)
+    Red_image=cd45,     # section B — CD45       (red)
+    Brown_image=ecad,   # section C — E-cadherin (membrane,   brown)
+    blue_name="DNA", red_name="CD45", brown_name="E-cadherin",
+    blue_bar=True, red_bar=True, brown_bar=True,
+    save_dir="out/virtual_multiplex.png",
+)
+```
+</details>
+
+# Citation
+
+If you use **IMC-HistoTools** in your research, please cite the Se IMC paper (citation
+to be added upon publication).
+
+# License
+
+This project is licensed under the **MIT License** — see the [LICENSE](LICENSE) file.

imc_histotools-0.1.0/__init__.py

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+"""
+IMC-HistoTools — digital pathology analysis toolkit for the Selenium (Se) IMC paper.
+
+Provides:
+  * virtual_IHC            : Beer-Lambert virtual IHC (brightfield-like) rendering
+  * virtual_IHC_ROI        : local-region rendering that keeps original pixel coords
+  * virtual_IHC_annotation : Qupath geojson -> ROI masks
+  * Hscore_threshold       : median-intensity thresholds from Np/Lp/Mp/Hp reference ROIs
+  * pix_Hscore_map         : pixel-wise H-score classification + CSV + figures
+"""
+
+from .virtual_IHC import virtual_IHC, virtual_IHC_ROI
+from .annotation_region import virtual_IHC_annotation, Hscore_threshold
+from .pix_Hscore import pix_Hscore_map
+
+__version__ = "0.1.0"
+
+__all__ = [
+    "virtual_IHC",
+    "virtual_IHC_ROI",
+    "virtual_IHC_annotation",
+    "Hscore_threshold",
+    "pix_Hscore_map",
+]

imc_histotools-0.1.0/annotation_region.py

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+"""
+annotation_region.py — Qupath 圈画 ROI 与 H-score 阈值模块 (IMC-HistoTools)
+
+提供:
+  * ``virtual_IHC_annotation`` : 读取 Qupath geojson 圈画文件 → 栅格化为 ROI mask
+  * ``Hscore_threshold``       : 根据参考 ROI (Np / Lp / Mp / Hp) 计算各层
+                                 像素中位值, 作为 pixel-wise H-score 分层阈值
+
+对应 2610/261003_Pix_Hscore_histopathology.ipynb 中的 geojson → mask 逻辑,
+并扩展为可直接复用的包函数。
+"""
+
+import json
+from pathlib import Path
+
+import numpy as np
+import cv2
+
+
+# ============================================================
+# helper
+# ============================================================
+
+def _as_mask(roi, shape):
+    """把「单个 mask 或 mask 列表」归一化为一个 bool ndarray (列表取并集)."""
+    if roi is None:
+        return None
+    if isinstance(roi, (list, tuple)):
+        m = np.zeros(shape, dtype=bool)
+        for r in roi:
+            if r is None:
+                continue
+            m |= np.asarray(r, dtype=bool)
+        return m
+    return np.asarray(roi, dtype=bool)
+
+
+# ============================================================
+# 1. Qupath geojson → ROI mask
+# ============================================================
+
+def virtual_IHC_annotation(image, geojson_path, region_order=None, name_key='name'):
+    """
+    读取 Qupath geojson 圈画文件, 栅格化为 ROI 区域的布尔 mask。
+
+    仅取每个 polygon 的外环 (第一个坐标环), 用 ``cv2.fillPoly`` 填充;
+    支持 Polygon 与 MultiPolygon。
+
+    Parameters
+    ----------
+    image : 2D ndarray 或 (H, W) tuple
+        用于确定栅格尺寸 H, W (通常传入对应的 virtual IHC / marker 图像)。
+    geojson_path : str or Path
+        Qupath 导出的 .geojson 文件路径。
+    region_order : list of str or None
+        返回结果的 region 顺序; None → 按 geojson 中出现顺序去重。
+    name_key : str
+        feature['properties'] 中用于区分区域名称的键 (默认 'name')。
+
+    Returns
+    -------
+    dict
+        {
+          'polys' : {name: [xy ndarray (N,2), ...]},   # 每个区域的外环顶点 (x, y)
+          'masks' : {name: bool ndarray (H, W)},       # 每个区域的栅格 mask
+          'names' : [按顺序的 region 名],
+        }
+    """
+    image = np.asarray(image)
+    if image.ndim == 2:
+        H, W = image.shape
+    else:
+        H, W = int(image[0]), int(image[1])
+
+    with open(geojson_path) as f:
+        gj = json.load(f)
+
+    region_polys = {}              # name -> [exterior xy array, ...]
+    for feat in gj['features']:
+        name = feat['properties'].get(name_key, 'unknown')
+        geom = feat['geometry']
+        if geom['type'] == 'MultiPolygon':
+            polys = geom['coordinates']
+        else:
+            polys = [geom['coordinates']]
+        for poly in polys:
+            # 外环 (x, y)
+            region_polys.setdefault(name, []).append(
+                np.asarray(poly[0], dtype=np.float64))
+
+    if region_order is None:
+        region_order = list(region_polys.keys())
+
+    region_masks = {}
+    for name in region_order:
+        m = np.zeros((H, W), np.uint8)
+        for xy in region_polys.get(name, []):
+            pts = np.round(xy).astype(np.int32).reshape(-1, 1, 2)   # cv2: (x, y)
+            cv2.fillPoly(m, [pts], 1)
+        region_masks[name] = m.astype(bool)
+
+    return {
+        'polys': {n: region_polys.get(n, []) for n in region_order},
+        'masks': region_masks,
+        'names': region_order,
+    }
+
+
+# ============================================================
+# 2. 参考 ROI → H-score 分层阈值 (中位值)
+# ============================================================
+
+def Hscore_threshold(marker_image, Np=None, Lp=None, Mp=None, Hp=None,
+                     tissue_mask=None, exclude_zero=False, stat='median'):
+    """
+    根据参考 ROI (Np / Lp / Mp / Hp) 统计像素强度, 作为返回的阈值。
+
+    对每个参考 ROI 分别统计:
+      - mean    : 平均值
+      - median  : 中位值
+      - geomean : 几何平均值 (仅正像素)
+      - all     : mean / median / geomean 三者的平均
+
+    Np / Lp / Mp / Hp 分别对应单个或多个设置 ROI 区域 (bool mask 或 mask 列表,
+    列表取并集); 可传 ``tissue_mask`` 以仅统计落在组织内的像素。
+
+    Parameters
+    ----------
+    marker_image : 2D ndarray
+        marker 强度图像 (通常为背景扣除后的图像)。
+    Np, Lp, Mp, Hp : bool ndarray 或 list of bool ndarray, 或 None
+        负 / 低 / 中 / 高 表达的参考 ROI 区域。
+    tissue_mask : bool ndarray or None
+        组织 mask (True=组织); 提供时各 ROI 会与组织求交。
+    exclude_zero : bool
+        是否在统计前排除强度为 0 的像素 (默认 False)。
+    stat : str, {'mean','median','geomean','all'}
+        选择用于 ``thresholds`` 的统计量 (默认 'median')。
+
+    Returns
+    -------
+    dict
+        {
+          'Np' : {'mean','median','geomean','all'} 或 None,
+          'Lp' : {...}, 'Mp' : {...}, 'Hp' : {...},
+          'thresholds' : (T1, T2, T3),   # 由 stat 决定, 对应 Lp/Mp/Hp
+          'stat' : str,
+        }
+    """
+    if stat not in ('mean', 'median', 'geomean', 'all'):
+        raise ValueError(f"stat 必须是 'mean'/'median'/'geomean'/'all', 得到 {stat!r}")
+
+    img = np.asarray(marker_image, dtype=np.float32)
+    shape = img.shape
+
+    def _stats(roi):
+        m = _as_mask(roi, shape)
+        if m is None:
+            return None
+        if tissue_mask is not None:
+            m = m & np.asarray(tissue_mask, dtype=bool)
+        vals = img[m].astype(np.float64)
+        if exclude_zero:
+            vals = vals[vals > 0]
+        if vals.size == 0:
+            return None
+        mean = float(np.mean(vals))
+        median = float(np.median(vals))
+        pos = vals[vals > 0]
+        geomean = float(np.exp(np.mean(np.log(pos)))) if pos.size else 0.0
+        all_ = (mean + median + geomean) / 3.0
+        return {'mean': mean, 'median': median, 'geomean': geomean, 'all': all_}
+
+    stats = {'Np': _stats(Np), 'Lp': _stats(Lp),
+             'Mp': _stats(Mp), 'Hp': _stats(Hp)}
+
+    thresholds = tuple(stats[k][stat] if stats[k] is not None else None
+                       for k in ('Lp', 'Mp', 'Hp'))
+
+    result = dict(stats)
+    result['thresholds'] = thresholds
+    result['stat'] = stat
+    return result