morphlabs 0.1.0__py3-none-any.whl

morphlabs/__init__.py

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+from .models import Scientia
+
+__version__ = "0.1.0"
+__all__ = ["Scientia"]

morphlabs/io/__init__.py

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+from .loading import EEGData
+
+__all__ = ['EEGData']

morphlabs/io/loading.py

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+import numpy as np
+import pandas as pd
+import mne
+from pathlib import Path
+from typing import Optional
+
+
+class EEGData:
+    def __init__(self, file_path: str):
+        self.file_path = file_path
+        self._data = None
+        self._channels = None
+        self._pad_amount = None
+
+        if file_path is not None:
+            if not self.load_data():
+                raise ValueError(f"Failed to load data from {file_path}")
+        
+    def get_data(self) -> Optional[list[np.ndarray]]:
+        return self._data
+
+    def get_channels(self) -> Optional[int]:
+        return self._channels
+
+    def get_pad_amount(self) -> Optional[int]:
+        return self._pad_amount
+
+    def load_data(self) -> bool:
+        self._validate_file_path(self.file_path)
+        match Path(self.file_path).suffix:
+            case '.csv':
+                self.load_data_from_csv(self.file_path)
+                return True
+            case '.edf':
+                self.load_data_from_edf(self.file_path)
+                return True
+            case '.bdf':
+                self.load_data_from_bdf(self.file_path)
+                return True
+            case _:
+                raise ValueError(f"Unsupported file type: {str(self.file_path).split('.')[-1]}, please use .csv, .edf, or .bdf files.") 
+    
+    def load_data_from_csv(self, file_path: str):
+        try:
+            data = pd.read_csv(file_path)
+            if data.empty:
+                raise ValueError(f"File is empty: '{file_path}'. Please provide a file with EEG data.")
+            self._channels = len(data.columns)
+            self._data, self._pad_amount = self.segment_data(data.values.T.astype(np.float32))
+            self.verify_montage()
+        except UnicodeDecodeError as e:
+            raise ValueError(f"Failed to load CSV file '{file_path}': File contains invalid characters. Details: {e}")
+        except pd.errors.ParserError as e:
+            raise ValueError(f"Failed to parse CSV file '{file_path}': File may be corrupted or incorrectly formatted. Details: {e}")
+        except pd.errors.EmptyDataError:
+            raise ValueError(f"File is empty: '{file_path}'. Please provide a file with EEG data.")
+        except ValueError:
+            raise
+        except Exception as e:
+            raise ValueError(f"Failed to load CSV file '{file_path}': {type(e).__name__}: {e}")
+
+    def load_data_from_edf(self, file_path: str):
+        try:
+            raw = mne.io.read_raw_edf(file_path, preload=True, verbose=False)
+            self._channels = len(raw.ch_names)
+            self._data, self._pad_amount = self.segment_data(raw.get_data().astype(np.float32))
+            self.verify_montage()
+        except ValueError:
+            raise
+        except Exception as e:
+            raise ValueError(f"Failed to load EDF file '{file_path}': File may be corrupted or not a valid EDF format. Details: {type(e).__name__}: {e}")
+
+    def load_data_from_bdf(self, file_path: str):
+        try:
+            raw = mne.io.read_raw_bdf(file_path, preload=True, verbose=False)
+            self._channels = len(raw.ch_names)
+            self._data, self._pad_amount = self.segment_data(raw.get_data().astype(np.float32))
+            self.verify_montage()
+        except ValueError:
+            raise
+        except Exception as e:
+            raise ValueError(f"Failed to load BDF file '{file_path}': File may be corrupted or not a valid BDF format. Details: {type(e).__name__}: {e}")
+
+    def _validate_file_path(self, file_path: str) -> None:
+        path = Path(file_path)
+
+        if not path.exists():
+            raise ValueError(f"File not found: '{file_path}'. Please check the file path exists.")
+        if not path.is_file():
+            raise ValueError(f"Path is not a file: '{file_path}'. Please provide a path to a file, not a directory.")
+        if path.stat().st_size == 0:
+            raise ValueError(f"File is empty: '{file_path}'. Please provide a file with EEG data.")
+
+    def segment_data(self, data: np.ndarray) -> tuple[list[np.ndarray], int]:
+        n_samples = data.shape[1]
+        window_size = 1000  
+        segments = []
+        pad_amount = 0
+
+        for i in range(0, n_samples, window_size):
+            segment = data[:, i:i+window_size]
+            if segment.shape[1] != window_size:
+                pad_amount = window_size - segment.shape[1]
+                pad_width = ((0, 0), (0, pad_amount))
+                segment = np.pad(segment, pad_width, 'constant')
+            segments.append(segment)
+        return segments, pad_amount
+
+
+    def verify_montage(self) -> None:
+        if self._channels != 19:
+            raise ValueError(f"Unsupported number of channels: {self._channels}, Scientia currently only supports the 19 channels in the 10-20 system.")

morphlabs/models/__init__.py

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+from .scientia import Scientia
+
+__all__ = ['Scientia']

morphlabs/models/scientia.py

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+import requests
+import numpy as np
+import os
+import logging
+from typing import Optional
+from tenacity import retry, stop_after_attempt, wait_exponential, retry_if_exception_type
+
+from morphlabs.io.loading import EEGData
+
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+API_ERROR_MESSAGES = {
+    400: "Bad request: The data sent to the API was invalid. Please check your input data format.",
+    401: "Authentication failed: Invalid API key. Please check your SCIENTIA_API_KEY.",
+    403: "Access denied: Your API key does not have permission for this operation. Please contact support.",
+    404: "API endpoint not found: Please check the base_url configuration.",
+    429: "Rate limit exceeded: Too many requests. Please wait a moment and try again.",
+    500: "Server error: The Scientia API encountered an internal error. Please try again later.",
+    502: "Bad gateway: The Scientia API is temporarily unavailable. Please try again later.",
+    503: "Service unavailable: The Scientia API is temporarily down for maintenance. Please try again later.",
+    504: "Gateway timeout: The request took too long. Please try again with smaller data segments.",
+}
+
+RETRYABLE_STATUS_CODES = [429, 500, 502, 503, 504]
+
+RUNPOD_API_KEY = "rpa_FFBJYB2SODF8Z3MCXWY5W78L8KI0A4BGQ999JLUZcqkk9u"
+
+
+class RetryableAPIError(Exception):
+    pass
+
+class Scientia:
+    def __init__(self, api_key: Optional[str] = None, base_url: Optional[str] = None):
+        api_key = api_key if api_key is not None else os.getenv("SCIENTIA_API_KEY")
+
+        if api_key is not None and not api_key.strip():
+            raise ValueError("API key cannot be empty or whitespace. Please provide a valid API key.")
+        self.api_key = api_key
+
+        if base_url is not None:
+            if not base_url.startswith(("http://", "https://")):
+                raise ValueError(f"Invalid base_url: '{base_url}'. URL must start with http:// or https://")
+            self.base_url = base_url.rstrip("/")
+        else:
+            self.base_url = "https://api.runpod.ai/v2/9ni9hifywn9z73/runsync"
+
+    def clean_data(self, data_path: str) -> np.ndarray:
+
+        if self.api_key is None:
+            raise ValueError("API key not found. Please pass the API key as an argument or set the SCIENTIA_API_KEY environment variable.")
+
+        data_obj = EEGData(data_path)
+
+        data_samples = data_obj.get_data()
+        pad_amount = data_obj.get_pad_amount()
+
+        cleaned_samples = []
+
+        logger.info(f"Cleaning {len(data_samples) * 1000  - pad_amount} samples")
+        for i, sample in enumerate(data_samples):
+            
+            response = self._make_api_request(
+                url=self.base_url,
+                json={"input": {"api_key": self.api_key, "data": sample.tolist()}},
+                timeout=30
+            )
+
+
+            logger.info(f"Cleaned {(i + 1) * 1000} of {len(data_samples)*1000 - pad_amount} samples")
+
+            # Validate response structure
+            try:
+                response_data = response.json()
+            except requests.exceptions.JSONDecodeError:
+                raise ValueError("Invalid response from API: Expected JSON but received invalid data.")
+
+            # Handle RunPod response format
+            status = response_data.get("status")
+            if status != "COMPLETED":
+                if status in ("IN_QUEUE", "IN_PROGRESS"):
+                    raise ValueError(f"Scientia API request is still processing (status: {status}). Please try again.")
+                elif status == "FAILED":
+                    error_msg = response_data.get("error", "Unknown error")
+                    raise ValueError(f"Scientia API request failed: {error_msg}")
+                elif status == "CANCELLED":
+                    raise ValueError("Scientia API request was cancelled.")
+                else:
+                    raise ValueError(f"Unexpected response status from Scientia API: {status}")
+
+            output = response_data.get("output")
+            if output is None or "reconstructed" not in output:
+                raise ValueError("Invalid response from API: Missing 'reconstructed' field in response.")
+
+            cleaned_sample = np.array(output['reconstructed'])
+            if i == len(data_samples) - 1 and pad_amount > 0:
+                cleaned_sample = cleaned_sample[:,:-pad_amount]
+            cleaned_samples.append(cleaned_sample)
+
+        return self._reconstruct_data(cleaned_samples)
+
+    def _reconstruct_data(self, cleaned_samples: list[np.ndarray]) -> np.ndarray:
+        return np.concatenate(cleaned_samples, axis=1)
+
+    @retry(stop=stop_after_attempt(3), wait=wait_exponential(multiplier=1, min=4, max=15), retry=retry_if_exception_type(RetryableAPIError))
+    def _make_api_request(self, url: str, json: dict, timeout: int) -> requests.Response:
+        headers = {"Authorization": f"Bearer {RUNPOD_API_KEY}"}
+        try:
+            response = requests.post(url, headers=headers, json=json, timeout=timeout)
+        except (requests.exceptions.Timeout, requests.exceptions.ConnectionError) as e:
+            raise RetryableAPIError(f"Network error: {e}")
+
+        if response.status_code in RETRYABLE_STATUS_CODES:
+            raise RetryableAPIError(f"API request failed with status {response.status_code}: {response.text}")
+
+        if not response.ok:
+            error_msg = API_ERROR_MESSAGES.get(response.status_code, f"API request failed with status {response.status_code}: {response.text}")
+            raise ValueError(error_msg)
+
+        return response

morphlabs-0.1.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: morphlabs
+Version: 0.1.0
+Summary: Python SDK for Morphlabs biosignal processing API
+Author-email: Morphlabs <support@morphlabs.tech>
+Maintainer-email: Morphlabs <support@morphlabs.tech>
+License-Expression: MIT
+Project-URL: Homepage, https://morphlabs.tech
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.20.0
+Requires-Dist: requests>=2.28.0
+Requires-Dist: mne>=1.0.0
+Requires-Dist: pandas>=1.3.0
+Requires-Dist: scipy>=1.7.0
+Requires-Dist: tenacity>=9.1.2
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Dynamic: license-file
+
+# morphlabs
+
+Python SDK for Morphlabs biosignal processing API.
+
+## Installation
+
+```bash
+pip install morphlabs
+```
+
+## Quick Start
+
+```python
+from morphlabs.models import Scientia
+
+# Set SCIENTIA_API_KEY environment variable or pass directly
+scientia = Scientia(api_key="your-api-key")
+
+# Clean EEG data
+cleaned_data = scientia.clean_data("path/to/eeg_file.csv")
+```
+
+## Documentation
+
+For full documentation, see [docs.morphlabs.tech](https://docs.morphlabs.tech)
+
+## License
+
+MIT

morphlabs-0.1.0.dist-info/RECORD

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+morphlabs/__init__.py,sha256=bo9Lfd9DLJ38e0oJ-81hFxSY3mYxkDv9Ex-TVAf6s88,74
+morphlabs/io/__init__.py,sha256=2ZCMfJxqr_FBUsWrlne-OI_VPVsv8UVar6IdpX_L7Bk,51
+morphlabs/io/loading.py,sha256=YuRCZiA7YjZ_C7IKwtHiP-CbTBulciBHydxw4c-Ielw,4766
+morphlabs/models/__init__.py,sha256=jLRf8mLI6-tyIum6UWRg8G6Hlt6QRaWJETJKDfyz1CQ,54
+morphlabs/models/scientia.py,sha256=uU598F0m2L7S8i7KC9l_KP8XdBhQngPV4YqIWnBsBQY,5557
+morphlabs-0.1.0.dist-info/licenses/LICENSE,sha256=BP9UXesZoxQDMPkeCn9j59qgYkvRqUupKvZlyXHUgHs,1066
+morphlabs-0.1.0.dist-info/METADATA,sha256=cNNPCUmGWnXEHKc-n_1d4s4q3fHcXL_xlaMb_kaECm4,1155
+morphlabs-0.1.0.dist-info/WHEEL,sha256=YLJXdYXQ2FQ0Uqn2J-6iEIC-3iOey8lH3xCtvFLkd8Q,91
+morphlabs-0.1.0.dist-info/top_level.txt,sha256=_Ox5cybZgvO8ipJ_zaFfmbamnqwqsLGn-PxXyP343Vs,10
+morphlabs-0.1.0.dist-info/RECORD,,

morphlabs-0.1.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: setuptools (81.0.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

morphlabs-0.1.0.dist-info/licenses/LICENSE

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+MIT License
+
+Copyright (c) 2025 Morphlabs
+
+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.

morphlabs-0.1.0.dist-info/top_level.txt

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+morphlabs