fastccm 0.2.3a1__tar.gz

fastccm-0.2.3a1/LICENSE

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+MIT License
+
+Copyright (c) 2025 Iaroslav Korobov
+
+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.

fastccm-0.2.3a1/MANIFEST.in

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+include README.md
+include LICENSE
+recursive-include src *.py

fastccm-0.2.3a1/PKG-INFO

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+Metadata-Version: 2.4
+Name: fastccm
+Version: 0.2.3a1
+Summary: A package for optimized Convergent Cross Mapping using PyTorch.
+Author: Iaroslav Korobov
+License: MIT License
+        
+        Copyright (c) 2025 Iaroslav Korobov
+        
+        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.
+        
+Project-URL: Homepage, https://github.com/z7743/FastCCM
+Project-URL: Issues, https://github.com/z7743/FastCCM/issues
+Classifier: License :: OSI Approved :: MIT License
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.23
+Requires-Dist: scipy>=1.10
+Requires-Dist: scikit-learn>=1.3
+Requires-Dist: matplotlib>=3.5
+Requires-Dist: pandas>=1.5
+Dynamic: license-file
+
+# FastCCM
+PyTorch-based implementation of Convergent Cross Mapping (CCM) optimized for calculating pairwise CCM matrices.
+
+## Installation
+
+**Requirements**: Python ≥ 3.9, pip.
+
+**CPU-only:**
+```bash
+pip install --upgrade pip
+pip install torch==2.3.1 --index-url https://download.pytorch.org/whl/cpu
+pip install "fastccm @ git+https://github.com/z7743/FastCCM.git@v0.2.2"
+```
+
+**CUDA:**
+```bash
+pip install --upgrade pip
+pip install torch==2.3.1 --index-url https://download.pytorch.org/whl/cu121
+pip install "fastccm @ git+https://github.com/z7743/FastCCM.git@v0.2.2"
+```
+
+**macOS (CPU/MPS):**
+```bash
+pip install --upgrade pip
+pip install torch==2.3.1
+pip install "fastccm @ git+https://github.com/z7743/FastCCM.git@v0.2.2"
+```
+
+## Quick start
+
+This example demonstrates how to use the FastCCM package for performing Convergent Cross Mapping (CCM).
+
+1. Import Required Libraries
+
+```python
+from fastccm import PairwiseCCM, utils
+from fastccm.data import get_truncated_rossler_lorenz_rand
+import numpy as np
+```
+
+2. Initialize the CCM Object
+
+Specify the device to use (e.g., "cpu" or "cuda"):
+
+```python
+ccm = PairwiseCCM(device="cpu")
+```
+
+3. Generate Data
+
+```python
+# Generate a joint Rossler-Lorenz data
+X = get_truncated_rossler_lorenz_rand(400, 20000, alpha=6, C=2, seed=0)
+
+Rossler_emb = utils.embed(X[:, 0], E = 7, tau = 4)   # see find_optimal_embedding_params
+Lorenz_emb  = utils.embed(X[:, 3], E = 8, tau = 9)
+
+print(f"Rossler embedding shape: {Rossler_emb.shape}")
+print(f"Lorenz embedding shape: {Lorenz_emb.shape}")
+
+```
+![alt text](docs/img/rossler_lorenz.png)
+
+### Calculate cross-mapping prediction
+
+```python
+# Rossler cross-mapping Lorenz
+result_rossler_xmap_lorenz = ccm.score_matrix(
+    X_emb=Rossler_emb, 
+    Y_emb=Lorenz_emb, 
+    library_size=None,  # use maximum points
+    sample_size=300,    # use 300 random points to estimate the score
+    exclusion_window=50, 
+    tp=0, 
+    method="simplex",
+    seed=0
+)
+
+# Lorenz cross-mapping Rossler
+result_lorenz_xmap_rossler = ccm.score_matrix(
+    X_emb=Lorenz_emb, 
+    Y_emb=Rossler_emb, 
+    library_size=None, 
+    sample_size=300, 
+    exclusion_window=50, 
+    tp=0, 
+    method="simplex",
+    seed=0
+)
+
+print(f"Rossler xmap Lorenz. Shape: {result_rossler_xmap_lorenz.shape}, score: {result_rossler_xmap_lorenz[-1,0,0]:.3f}")
+print(f"Lorenz xmap Rossler. Shape: {result_lorenz_xmap_rossler.shape}, score: {result_lorenz_xmap_rossler[-1,0,0]:.3f}")
+
+```
+
+### Test convergence
+
+```python
+from fastccm import ccm_utils
+
+conv_test_res = ccm_utils.Functions("cpu").convergence_test(
+    X_emb=Rossler_emb, 
+    Y_emb=Lorenz_emb,
+    library_sizes=[160, 320, 640, 1250, 2500, 5000, 10000, 20000],
+    sample_size=1000, 
+    exclusion_window=50, 
+    tp=0, 
+    method="simplex", 
+    trials=20,
+    seed=0
+)
+```
+
+Plot the convergence test results:
+```python
+ccm_utils.Visualizer().plot_convergence_test(conv_test_res)
+```
+
+![alt text](docs/img/conv_test.png)
+
+### Find optimal time-delay embedding parameters
+```python
+
+optimal_E_tau_res = ccm_utils.Functions("cpu").find_optimal_embedding_params(
+    X[:,3], 
+    library_size=4000, 
+    sample_size=300, 
+    exclusion_window=50,
+    E_range=np.arange(2,30),
+    tau_range=np.arange(1,30),
+    tp_max=50,
+    method="simplex",
+    seed=0
+)
+
+print(f"Optimal E: {optimal_E_tau_res['optimal_E']}, optimal_tau: {optimal_E_tau_res['optimal_tau']}")
+```
+
+Plot the results
+```python
+ccm_utils.Visualizer().visualize_optimal_e_tau(optimal_E_tau_res)
+```
+
+![alt text](docs/img/e_tau_test.png)

fastccm-0.2.3a1/README.md

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+# FastCCM
+PyTorch-based implementation of Convergent Cross Mapping (CCM) optimized for calculating pairwise CCM matrices.
+
+## Installation
+
+**Requirements**: Python ≥ 3.9, pip.
+
+**CPU-only:**
+```bash
+pip install --upgrade pip
+pip install torch==2.3.1 --index-url https://download.pytorch.org/whl/cpu
+pip install "fastccm @ git+https://github.com/z7743/FastCCM.git@v0.2.2"
+```
+
+**CUDA:**
+```bash
+pip install --upgrade pip
+pip install torch==2.3.1 --index-url https://download.pytorch.org/whl/cu121
+pip install "fastccm @ git+https://github.com/z7743/FastCCM.git@v0.2.2"
+```
+
+**macOS (CPU/MPS):**
+```bash
+pip install --upgrade pip
+pip install torch==2.3.1
+pip install "fastccm @ git+https://github.com/z7743/FastCCM.git@v0.2.2"
+```
+
+## Quick start
+
+This example demonstrates how to use the FastCCM package for performing Convergent Cross Mapping (CCM).
+
+1. Import Required Libraries
+
+```python
+from fastccm import PairwiseCCM, utils
+from fastccm.data import get_truncated_rossler_lorenz_rand
+import numpy as np
+```
+
+2. Initialize the CCM Object
+
+Specify the device to use (e.g., "cpu" or "cuda"):
+
+```python
+ccm = PairwiseCCM(device="cpu")
+```
+
+3. Generate Data
+
+```python
+# Generate a joint Rossler-Lorenz data
+X = get_truncated_rossler_lorenz_rand(400, 20000, alpha=6, C=2, seed=0)
+
+Rossler_emb = utils.embed(X[:, 0], E = 7, tau = 4)   # see find_optimal_embedding_params
+Lorenz_emb  = utils.embed(X[:, 3], E = 8, tau = 9)
+
+print(f"Rossler embedding shape: {Rossler_emb.shape}")
+print(f"Lorenz embedding shape: {Lorenz_emb.shape}")
+
+```
+![alt text](docs/img/rossler_lorenz.png)
+
+### Calculate cross-mapping prediction
+
+```python
+# Rossler cross-mapping Lorenz
+result_rossler_xmap_lorenz = ccm.score_matrix(
+    X_emb=Rossler_emb, 
+    Y_emb=Lorenz_emb, 
+    library_size=None,  # use maximum points
+    sample_size=300,    # use 300 random points to estimate the score
+    exclusion_window=50, 
+    tp=0, 
+    method="simplex",
+    seed=0
+)
+
+# Lorenz cross-mapping Rossler
+result_lorenz_xmap_rossler = ccm.score_matrix(
+    X_emb=Lorenz_emb, 
+    Y_emb=Rossler_emb, 
+    library_size=None, 
+    sample_size=300, 
+    exclusion_window=50, 
+    tp=0, 
+    method="simplex",
+    seed=0
+)
+
+print(f"Rossler xmap Lorenz. Shape: {result_rossler_xmap_lorenz.shape}, score: {result_rossler_xmap_lorenz[-1,0,0]:.3f}")
+print(f"Lorenz xmap Rossler. Shape: {result_lorenz_xmap_rossler.shape}, score: {result_lorenz_xmap_rossler[-1,0,0]:.3f}")
+
+```
+
+### Test convergence
+
+```python
+from fastccm import ccm_utils
+
+conv_test_res = ccm_utils.Functions("cpu").convergence_test(
+    X_emb=Rossler_emb, 
+    Y_emb=Lorenz_emb,
+    library_sizes=[160, 320, 640, 1250, 2500, 5000, 10000, 20000],
+    sample_size=1000, 
+    exclusion_window=50, 
+    tp=0, 
+    method="simplex", 
+    trials=20,
+    seed=0
+)
+```
+
+Plot the convergence test results:
+```python
+ccm_utils.Visualizer().plot_convergence_test(conv_test_res)
+```
+
+![alt text](docs/img/conv_test.png)
+
+### Find optimal time-delay embedding parameters
+```python
+
+optimal_E_tau_res = ccm_utils.Functions("cpu").find_optimal_embedding_params(
+    X[:,3], 
+    library_size=4000, 
+    sample_size=300, 
+    exclusion_window=50,
+    E_range=np.arange(2,30),
+    tau_range=np.arange(1,30),
+    tp_max=50,
+    method="simplex",
+    seed=0
+)
+
+print(f"Optimal E: {optimal_E_tau_res['optimal_E']}, optimal_tau: {optimal_E_tau_res['optimal_tau']}")
+```
+
+Plot the results
+```python
+ccm_utils.Visualizer().visualize_optimal_e_tau(optimal_E_tau_res)
+```
+
+![alt text](docs/img/e_tau_test.png)

fastccm-0.2.3a1/pyproject.toml

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+[build-system]
+requires = ["setuptools>=69", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "fastccm"
+dynamic = ["version"]
+description = "A package for optimized Convergent Cross Mapping using PyTorch."
+readme = { file = "README.md", content-type = "text/markdown" }
+requires-python = ">=3.9"
+license = { file = "LICENSE" }
+classifiers = ["License :: OSI Approved :: MIT License"]
+authors = [{ name = "Iaroslav Korobov" }]
+
+dependencies = [
+  "numpy>=1.23",
+  "scipy>=1.10",
+  "scikit-learn>=1.3",
+  "matplotlib>=3.5",
+  "pandas>=1.5",
+]
+
+[project.urls]
+Homepage = "https://github.com/z7743/FastCCM"
+Issues = "https://github.com/z7743/FastCCM/issues"
+
+[tool.setuptools.dynamic]
+version = { attr = "fastccm._version.__version__" }
+
+[tool.setuptools.packages.find]
+where = ["src"]

fastccm-0.2.3a1/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

fastccm-0.2.3a1/src/FastCCM.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: fastccm
+Version: 0.2.3a1
+Summary: A package for optimized Convergent Cross Mapping using PyTorch.
+Author: Iaroslav Korobov
+License: MIT License
+        
+        Copyright (c) 2025 Iaroslav Korobov
+        
+        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.
+        
+Project-URL: Homepage, https://github.com/z7743/FastCCM
+Project-URL: Issues, https://github.com/z7743/FastCCM/issues
+Classifier: License :: OSI Approved :: MIT License
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.23
+Requires-Dist: scipy>=1.10
+Requires-Dist: scikit-learn>=1.3
+Requires-Dist: matplotlib>=3.5
+Requires-Dist: pandas>=1.5
+Dynamic: license-file
+
+# FastCCM
+PyTorch-based implementation of Convergent Cross Mapping (CCM) optimized for calculating pairwise CCM matrices.
+
+## Installation
+
+**Requirements**: Python ≥ 3.9, pip.
+
+**CPU-only:**
+```bash
+pip install --upgrade pip
+pip install torch==2.3.1 --index-url https://download.pytorch.org/whl/cpu
+pip install "fastccm @ git+https://github.com/z7743/FastCCM.git@v0.2.2"
+```
+
+**CUDA:**
+```bash
+pip install --upgrade pip
+pip install torch==2.3.1 --index-url https://download.pytorch.org/whl/cu121
+pip install "fastccm @ git+https://github.com/z7743/FastCCM.git@v0.2.2"
+```
+
+**macOS (CPU/MPS):**
+```bash
+pip install --upgrade pip
+pip install torch==2.3.1
+pip install "fastccm @ git+https://github.com/z7743/FastCCM.git@v0.2.2"
+```
+
+## Quick start
+
+This example demonstrates how to use the FastCCM package for performing Convergent Cross Mapping (CCM).
+
+1. Import Required Libraries
+
+```python
+from fastccm import PairwiseCCM, utils
+from fastccm.data import get_truncated_rossler_lorenz_rand
+import numpy as np
+```
+
+2. Initialize the CCM Object
+
+Specify the device to use (e.g., "cpu" or "cuda"):
+
+```python
+ccm = PairwiseCCM(device="cpu")
+```
+
+3. Generate Data
+
+```python
+# Generate a joint Rossler-Lorenz data
+X = get_truncated_rossler_lorenz_rand(400, 20000, alpha=6, C=2, seed=0)
+
+Rossler_emb = utils.embed(X[:, 0], E = 7, tau = 4)   # see find_optimal_embedding_params
+Lorenz_emb  = utils.embed(X[:, 3], E = 8, tau = 9)
+
+print(f"Rossler embedding shape: {Rossler_emb.shape}")
+print(f"Lorenz embedding shape: {Lorenz_emb.shape}")
+
+```
+![alt text](docs/img/rossler_lorenz.png)
+
+### Calculate cross-mapping prediction
+
+```python
+# Rossler cross-mapping Lorenz
+result_rossler_xmap_lorenz = ccm.score_matrix(
+    X_emb=Rossler_emb, 
+    Y_emb=Lorenz_emb, 
+    library_size=None,  # use maximum points
+    sample_size=300,    # use 300 random points to estimate the score
+    exclusion_window=50, 
+    tp=0, 
+    method="simplex",
+    seed=0
+)
+
+# Lorenz cross-mapping Rossler
+result_lorenz_xmap_rossler = ccm.score_matrix(
+    X_emb=Lorenz_emb, 
+    Y_emb=Rossler_emb, 
+    library_size=None, 
+    sample_size=300, 
+    exclusion_window=50, 
+    tp=0, 
+    method="simplex",
+    seed=0
+)
+
+print(f"Rossler xmap Lorenz. Shape: {result_rossler_xmap_lorenz.shape}, score: {result_rossler_xmap_lorenz[-1,0,0]:.3f}")
+print(f"Lorenz xmap Rossler. Shape: {result_lorenz_xmap_rossler.shape}, score: {result_lorenz_xmap_rossler[-1,0,0]:.3f}")
+
+```
+
+### Test convergence
+
+```python
+from fastccm import ccm_utils
+
+conv_test_res = ccm_utils.Functions("cpu").convergence_test(
+    X_emb=Rossler_emb, 
+    Y_emb=Lorenz_emb,
+    library_sizes=[160, 320, 640, 1250, 2500, 5000, 10000, 20000],
+    sample_size=1000, 
+    exclusion_window=50, 
+    tp=0, 
+    method="simplex", 
+    trials=20,
+    seed=0
+)
+```
+
+Plot the convergence test results:
+```python
+ccm_utils.Visualizer().plot_convergence_test(conv_test_res)
+```
+
+![alt text](docs/img/conv_test.png)
+
+### Find optimal time-delay embedding parameters
+```python
+
+optimal_E_tau_res = ccm_utils.Functions("cpu").find_optimal_embedding_params(
+    X[:,3], 
+    library_size=4000, 
+    sample_size=300, 
+    exclusion_window=50,
+    E_range=np.arange(2,30),
+    tau_range=np.arange(1,30),
+    tp_max=50,
+    method="simplex",
+    seed=0
+)
+
+print(f"Optimal E: {optimal_E_tau_res['optimal_E']}, optimal_tau: {optimal_E_tau_res['optimal_tau']}")
+```
+
+Plot the results
+```python
+ccm_utils.Visualizer().visualize_optimal_e_tau(optimal_E_tau_res)
+```
+
+![alt text](docs/img/e_tau_test.png)

fastccm-0.2.3a1/src/FastCCM.egg-info/SOURCES.txt

@@ -0,0 +1,23 @@
+LICENSE
+MANIFEST.in
+README.md
+pyproject.toml
+src/FastCCM.egg-info/PKG-INFO
+src/FastCCM.egg-info/SOURCES.txt
+src/FastCCM.egg-info/dependency_links.txt
+src/FastCCM.egg-info/requires.txt
+src/FastCCM.egg-info/top_level.txt
+src/fastccm/__init__.py
+src/fastccm/_version.py
+src/fastccm/ccm.py
+src/fastccm/ccm_utils.py
+src/fastccm.egg-info/PKG-INFO
+src/fastccm.egg-info/SOURCES.txt
+src/fastccm.egg-info/dependency_links.txt
+src/fastccm.egg-info/requires.txt
+src/fastccm.egg-info/top_level.txt
+src/fastccm/data/__init__.py
+src/fastccm/data/data_loader.py
+src/fastccm/utils/__init__.py
+src/fastccm/utils/metrics.py
+src/fastccm/utils/utils.py

fastccm-0.2.3a1/src/FastCCM.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

fastccm-0.2.3a1/src/FastCCM.egg-info/requires.txt

@@ -0,0 +1,5 @@
+numpy>=1.23
+scipy>=1.10
+scikit-learn>=1.3
+matplotlib>=3.5
+pandas>=1.5

fastccm-0.2.3a1/src/FastCCM.egg-info/top_level.txt

@@ -0,0 +1 @@
+fastccm

fastccm-0.2.3a1/src/fastccm/__init__.py

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+# src/fastccm/__init__.py
+from importlib.metadata import version, PackageNotFoundError
+from typing import TYPE_CHECKING
+from ._version import __version__
+
+try:
+    __version__ = version("FastCCM")
+except PackageNotFoundError:
+    __version__ = "0.0.0"
+
+from . import data as data
+from . import utils as utils
+
+__all__ = ("__version__", "PairwiseCCM", "Visualizer", "Functions", "data", "utils")
+
+if TYPE_CHECKING:
+    from .ccm import PairwiseCCM as _PairwiseCCM
+    from .ccm_utils import Visualizer as _Visualizer, Functions as _Functions
+
+def __getattr__(name: str):
+    if name == "PairwiseCCM":
+        from .ccm import PairwiseCCM
+        return PairwiseCCM
+    if name == "Visualizer":
+        from .ccm_utils import Visualizer
+        return Visualizer
+    if name == "Functions":
+        from .ccm_utils import Functions
+        return Functions
+    raise AttributeError(f"module 'fastccm' has no attribute {name!r}")

fastccm-0.2.3a1/src/fastccm/_version.py

@@ -0,0 +1 @@
+__version__ = "0.2.3a1"