fix: spacing->f64

Author: plasma-blue

Cargo.lock

@@ -1,6 +1,6 @@
 [package]
 name = "mikan-rs"
-version = "0.1.3"
+version = "0.1.4"
 edition = "2021"
 license = "MIT OR Apache-2.0"
 description = "A medical image kit for segmentation metrics evaluation, native Rust support, and Python bindings for cross-language performance."

Cargo.toml

@@ -8,7 +8,7 @@ A **m**edical **i**mage **k**it for segment**a**tion metrics evaluatio**n**, nat
 
 - 🎯 **Simple**: The API is so intuitive that you can start using it immediately while reading the [documentation](https://github.com/Plasma-Blue/mikan-rs/blob/master/examples/tutorial.ipynb) in just one minute!
 
-- 🧮 **Comprehensive Metrics**: Easily to compute almost all of segmentation metrics:
+- 🧮 **Comprehensive Metrics**: Easily to compute almost all of segmentation metrics, **results are consistent with medpy**:
 
   - **Confusion Matrix Based:**
 
@@ -28,9 +28,18 @@ A **m**edical **i**mage **k**it for segment**a**tion metrics evaluatio**n**, nat
 
 ## 🔨 Install
 
-`cargo add mikan-rs` for rust project.
+For Rust projects, add the following to your `Cargo.toml`:
 
-`pip install mikan-rs` for python.
+```toml
+[dependencies]
+mikan-rs = "*"
+```
+
+For Python, install via pip:
+
+```sh
+pip install mikan-rs
+```
 
 ## 🥒 Develop
 
@@ -46,7 +55,7 @@ gt = sitk.ReadImage("gt.nii.gz", sitk.sitkUInt8)
 pred = sitk.ReadImage("pred.nii.gz", sitk.sitkUInt8)
 
 e = mikan.Evaluator(gt, pred)
-e.labels(1).metrics("dice")
+e.labels([1, 2, 3]).metrics(["dice", "hd", "hd95", "assd"])
 ```
 
 For details, please refer to the [python examples](https://github.com/Plasma-Blue/mikan-rs/blob/master/examples/tutorial.ipynb) and [rust examples](https://github.com/Plasma-Blue/mikan-rs/blob/master/examples/tutorial.rs).
@@ -73,9 +82,9 @@ A: They are wrong. Of course, we might be wrong too. PRs to fix issues are welco
 Licensed under either of the following licenses, at your choice:
 
 Apache License, Version 2.0
-(See LICENSE-APACHE or visit http://www.apache.org/licenses/LICENSE-2.0)
+(See LICENSE-APACHE or visit <http://www.apache.org/licenses/LICENSE-2.0>)
 
 MIT License
-(See LICENSE-MIT or visit http://opensource.org/licenses/MIT)
+(See LICENSE-MIT or visit <http://opensource.org/licenses/MIT>)
 
 Unless you explicitly state otherwise, any contribution intentionally submitted for inclusion in this project, as defined by the Apache License 2.0, will be dual-licensed under the above licenses without any additional terms or conditions.

README.md

@@ -101,7 +101,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 2,
    "metadata": {
     "id": "cxVnoqqEYd6F"
    },
@@ -125,14 +125,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "metadata": {
     "id": "E3lZFPFNYiSK"
    },
    "outputs": [],
    "source": [
-    "gt = sitk.ReadImage(\"patients_26_ground_truth.nii.gz\", sitk.sitkUInt8)\n",
-    "pred = sitk.ReadImage(\"patients_26_segmentation.nii.gz\", sitk.sitkUInt8)\n",
+    "gt = sitk.ReadImage(rf\"patients_26_ground_truth.nii.gz\", sitk.sitkUInt8)\n",
+    "pred = sitk.ReadImage(rf\"patients_26_segmentation.nii.gz\", sitk.sitkUInt8)\n",
     "\n",
     "gt_arr = sitk.GetArrayFromImage(gt)\n",
     "pred_arr = sitk.GetArrayFromImage(pred)\n",
@@ -154,7 +154,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 13,
    "metadata": {
     "colab": {
      "base_uri": "https://localhost:8080/"
@@ -167,9 +167,9 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Mikan cost 0.12 s.\n",
-      "medpy costs 0.19 s.\n",
-      "DSC: 1.54x faster\n"
+      "Mikan cost 0.03 s.\n",
+      "medpy costs 0.27 s.\n",
+      "DSC: 8.05x faster\n"
      ]
     }
    ],
@@ -201,7 +201,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 10,
    "metadata": {
     "colab": {
      "base_uri": "https://localhost:8080/"
@@ -214,27 +214,31 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Mikan has calculated Hausdorff distance and cost 4.47 s.\n",
+      "[3.8066796490554484, 5.875891921349948, 7.18959419428273, 55.03783156368531, 46.23897571237574]\n",
+      "Mikan has calculated Hausdorff distance and cost 0.93 s.\n",
       "Let's waiting for medpy, be patient for a while...\n",
-      "HD: 11.14x faster\n"
+      "46.23897571237574\n",
+      "HD: 71.22x faster\n"
      ]
     }
    ],
    "source": [
     "# mikan: HD\n",
     "t = time.time()\n",
     "evaluator = mikan.ArrayEvaluator(gt_arr, pred_arr, spacing=gt.GetSpacing())\n",
-    "hausdorff_distance = evaluator.labels([1,2,3,4,5]).metrics(\"HD\")\n",
+    "hausdorff_distance = evaluator.labels([1, 2, 3, 4, 5]).metrics(\"HD\")\n",
+    "print(hausdorff_distance)\n",
+    "\n",
     "mikan_costs = time.time() - t\n",
     "print(f\"Mikan has calculated Hausdorff distance and cost {mikan_costs:.2f} s.\")\n",
     "print(f\"Let's waiting for medpy, be patient for a while...\")\n",
     "\n",
     "# medpy: HD\n",
     "t = time.time()\n",
-    "for i in (1,2,3,4,5):\n",
+    "for i in (1, 2, 3, 4, 5):\n",
     "    hausdorff_distance = hd(pred_arr == i, gt_arr == i, voxelspacing=gt.GetSpacing()[::-1])\n",
     "medpy_costs = time.time() - t\n",
-    "\n",
+    "print(hausdorff_distance)\n",
     "print(f\"HD: {medpy_costs / mikan_costs :.2f}x faster\")"
    ]
   },
@@ -249,7 +253,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 9,
    "metadata": {
     "colab": {
      "base_uri": "https://localhost:8080/"
@@ -262,11 +266,11 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "{'1': {'hd': 3.8066790103912354, 'hd95': 0.7410011291503906, 'assd': 0.24823972582817078}, '2': {'hd': 5.875893592834473, 'hd95': 0.8939142823219299, 'assd': 0.30189621448516846}, '3': {'hd': 7.1895952224731445, 'hd95': 0.7410049438476562, 'assd': 0.29092279076576233}, '4': {'hd': 55.0378303527832, 'hd95': 0.7410011291503906, 'assd': 0.2536499500274658}, '5': {'hd': 46.238975524902344, 'hd95': 0.7410125732421875, 'assd': 0.27448806166648865}}\n",
-      "Mikan has calculated distance and cost 3.80 s.\n",
+      "{'1': {'hd': 3.8066796490554484, 'hd95': 0.7409999966621399, 'assd': 0.2482734556966591}, '2': {'hd': 5.875891921349948, 'hd95': 0.893913303991663, 'assd': 0.30188703831217684}, '3': {'hd': 7.18959419428273, 'hd95': 0.7409999966621399, 'assd': 0.29096373483885757}, '4': {'hd': 55.03783156368531, 'hd95': 0.7409999966621399, 'assd': 0.25367831066384994}, '5': {'hd': 46.23897571237574, 'hd95': 0.7409999966621399, 'assd': 0.27452537658032045}}\n",
+      "Mikan has calculated distance and cost 0.96 s.\n",
       "Let's waiting for medpy, be patient for a while...\n",
       "{1: {'hd': 3.8066796490554484, 'hd95': 0.7409999966621399, 'assd': 0.24827345569665876}, 2: {'hd': 5.875891921349948, 'hd95': 0.893913303991663, 'assd': 0.3018870383121832}, 3: {'hd': 7.18959419428273, 'hd95': 0.7409999966621399, 'assd': 0.2909637348388582}, 4: {'hd': 55.03783156368531, 'hd95': 0.7409999966621399, 'assd': 0.25367831066385055}, 5: {'hd': 46.23897571237574, 'hd95': 0.7409999966621399, 'assd': 0.2745253765803193}}\n",
-      "Distances: 39.67x faster\n"
+      "Distances: 210.35x faster\n"
      ]
     }
    ],
@@ -307,7 +311,15 @@
    "name": "python3"
   },
   "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
    "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
    "version": "3.12.3"
   }
  },