nubrain 0.0.0__tar.gz

nubrain-0.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: nubrain
+Version: 0.0.0
+Summary: NuBrain connect
+Project-URL: Homepage, https://github.com/ingo-m/nubrain-connect
+Author-email: nuBrain Team <hello@nubrain.io>
+License-Expression: MIT
+Requires-Python: >=3.10
+Requires-Dist: brainflow>=5.16.0
+Requires-Dist: certifi>=2025.4.26
+Requires-Dist: charset-normalizer>=3.4.2
+Requires-Dist: idna>=3.10
+Requires-Dist: numpy>=2.2.6
+Requires-Dist: pillow>=11.2.1
+Requires-Dist: pygame>=2.6.1
+Requires-Dist: requests>=2.32.3
+Requires-Dist: scipy>=1.15.3
+Requires-Dist: setuptools>=80.9.0
+Requires-Dist: urllib3>=2.4.0
+Description-Content-Type: text/markdown
+
+# nubrain-connect
+
+nubrain-connect

nubrain-0.0.0/README.md

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+# nubrain-connect
+
+nubrain-connect

nubrain-0.0.0/nubrain/example.py

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+def example():
+    print("Hello world")

nubrain-0.0.0/nubrain/experiment.py

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+import base64
+import datetime
+import glob
+import io
+import json
+import multiprocessing as mp
+import os
+import pickle
+import random
+from time import time
+
+import numpy as np
+import pygame
+import requests
+from brainflow.board_shim import BoardIds, BoardShim, BrainFlowInputParams
+from brainflow.data_filter import (
+    DataFilter,
+    DetrendOperations,
+    FilterTypes,
+)
+from PIL import Image
+from scipy.stats import zscore
+
+# --------------------------------------------------------------------------------------
+# *** Helper functions
+
+
+def load_and_scale_images(*, image_directory, screen_width, screen_height):
+    """
+    Loads all PNG and JPEG images from a directory and scales them to fit the screen.
+    """
+    extensions = ("*.png", "*.jpg", "*.jpeg")
+    image_files = []
+    for ext in extensions:
+        image_files.extend(glob.glob(os.path.join(image_directory, ext)))
+
+    loaded_images = []
+    if not image_files:
+        print(f"No images found in directory: {image_directory}")
+        return []
+
+    print(f"Found {len(image_files)} images.")
+
+    for filepath in image_files:
+        try:
+            img = pygame.image.load(filepath)
+            img_rect = img.get_rect()
+
+            # Calculate scaling factor to fit screen while maintaining aspect ratio
+            scale_w = screen_width / img_rect.width
+            scale_h = screen_height / img_rect.height
+            scale = min(scale_w, scale_h)
+
+            new_width = int(img_rect.width * scale)
+            new_height = int(img_rect.height * scale)
+
+            scaled_img = pygame.transform.smoothscale(img, (new_width, new_height))
+            loaded_images.append({"image_filepath": filepath, "image": scaled_img})
+            print(f"Loaded and scaled: {filepath}")
+        except pygame.error as e:
+            print(f"Error loading or scaling image {filepath}: {e}")
+    return loaded_images
+
+
+def resize_image(*, image_bytes, return_image_file_extension=False):
+    """
+    Resize image to maximal size before sending over network.
+    """
+    image = Image.open(io.BytesIO(image_bytes))
+
+    if image.format == "JPEG":
+        image_format = "JPEG"
+        image_file_extension = ".jpg"
+    elif image.format == "PNG":
+        image_format = "PNG"
+        image_file_extension = ".png"
+    elif image.format == "WEBP":
+        image_format = "WEBP"
+        image_file_extension = ".webp"
+    else:
+        print(f"Unexpected image format, will use png: {image.format}")
+        image_format = "PNG"
+        image_file_extension = ".png"
+
+    width, height = image.size
+
+    # Maximum dimension.
+    max_dimension = 256
+
+    # Check if resizing is needed.
+    if (width > max_dimension) or (height > max_dimension):
+        # Calculate the new size maintaining the aspect ratio.
+        if width > height:
+            new_width = max_dimension
+            new_height = int(max_dimension * height / width)
+        else:
+            new_height = max_dimension
+            new_width = int(max_dimension * width / height)
+
+        # Resize the image.
+        image = image.resize((new_width, new_height), Image.Resampling.BILINEAR)
+
+    # Convert the image to bytes.
+    img_byte_arr = io.BytesIO()
+
+    image.save(img_byte_arr, format=image_format)
+    img_byte_arr = bytearray(img_byte_arr.getvalue())
+
+    if return_image_file_extension:
+        return img_byte_arr, image_file_extension
+    else:
+        return img_byte_arr
+
+
+def get_formatted_current_datetime():
+    """
+    Returns the current date and time formatted as "YYYY-MM-DD-HHMMSS".
+
+    Returns:
+      str: The formatted date and time string.
+    """
+    now = datetime.datetime.now()
+    formatted_datetime = now.strftime("%Y-%m-%d-%H%M%S")
+    return formatted_datetime
+
+
+# --------------------------------------------------------------------------------------
+# *** Preprocessing & saving data
+
+
+def preprocess(subprocess_params: dict):
+    """
+    Preprocess data, send data to remote endpoint, and save copy locally. To be run in
+    separate process (using multiprocessing).
+    """
+    eeg_board_description = subprocess_params["eeg_board_description"]
+    eeg_sampling_rate = subprocess_params["eeg_sampling_rate"]
+    eeg_channels = subprocess_params["eeg_channels"]
+    eeg_channel_mapping = subprocess_params["eeg_channel_mapping"]
+
+    marker_channel = subprocess_params["marker_channel"]
+
+    bandstop_low_cutoff_freq = subprocess_params["bandstop_low_cutoff_freq"]
+    bandstop_high_cutoff_freq = subprocess_params["bandstop_high_cutoff_freq"]
+    bandstop_filter_order = subprocess_params["bandstop_filter_order"]
+
+    bandpass_low_cutoff_freq = subprocess_params["bandpass_low_cutoff_freq"]
+    bandpass_high_cutoff_freq = subprocess_params["bandpass_high_cutoff_freq"]
+    bandpass_filter_order = subprocess_params["bandpass_filter_order"]
+
+    nubrain_endpoint = subprocess_params["nubrain_endpoint"]
+    nubrain_api_key = subprocess_params["nubrain_api_key"]
+
+    path_out_data = subprocess_params["path_out_data"]
+
+    data_to_remote_queue = subprocess_params["data_to_remote_queue"]
+
+    experiment_data = {
+        "metadata": {
+            "eeg_board_description": eeg_board_description,
+            "eeg_sampling_rate": eeg_sampling_rate,
+            "eeg_channels": eeg_channels,
+            "eeg_channel_mapping": eeg_channel_mapping,
+            "bandstop_low_cutoff_freq": bandstop_low_cutoff_freq,
+            "bandstop_high_cutoff_freq": bandstop_high_cutoff_freq,
+            "bandstop_filter_order": bandstop_filter_order,
+            "bandpass_low_cutoff_freq": bandpass_low_cutoff_freq,
+            "bandpass_high_cutoff_freq": bandpass_high_cutoff_freq,
+            "bandpass_filter_order": bandpass_filter_order,
+            "time": time(),
+        },
+        "data": [],
+    }
+
+    counter = 0
+
+    while True:
+        data_to_send = data_to_remote_queue.get(block=True)
+
+        print(f"Data sender counter: {counter}")
+        counter += 1
+
+        if data_to_send is None:
+            # Received None. End process.
+            print("Ending preprocessing & data saving process.")
+            break
+
+        board_data = data_to_send["board_data"]
+        metadata = data_to_send["metadata"]
+        image_filepath = data_to_send["image_filepath"]
+
+        # ------------------------------------------------------------------------------
+        # *** Resize image
+
+        image = Image.open(image_filepath)
+
+        # Create a byte stream in memory.
+        byte_arr = io.BytesIO()
+
+        image.save(byte_arr, format="PNG")
+
+        # Get the byte value from the byte stream
+        image_bytes = byte_arr.getvalue()
+
+        # Limit image size.
+        current_image_bytes = resize_image(image_bytes=image_bytes)
+        # Encode in base64.
+        img_b64 = base64.b64encode(current_image_bytes).decode("utf-8")
+
+        # ------------------------------------------------------------------------------
+        # *** Filter
+
+        # When using brainflow, we can't filter a batch of all channels at once. Perhaps
+        # refactor and use scipy. Only filter EEG channels (not auxiliarry channels).
+        for idx_channel in eeg_channels:
+            # Apply detrending first (optional but often good practice for IIR filters)
+            DataFilter.detrend(board_data[idx_channel], DetrendOperations.LINEAR.value)
+            # Apply bandstop filter.
+            DataFilter.perform_bandstop(
+                data=board_data[idx_channel],
+                sampling_rate=eeg_sampling_rate,
+                start_freq=bandstop_low_cutoff_freq,
+                stop_freq=bandstop_high_cutoff_freq,
+                order=bandstop_filter_order,
+                filter_type=FilterTypes.BUTTERWORTH.value,
+                ripple=0.0,  # Ignored for Butterworth
+            )
+            # Apply bandpass filter.
+            # For FilterTypes.BUTTERWORTH, the ripple parameter is ignored (can be 0.0)
+            DataFilter.perform_bandpass(
+                data=board_data[idx_channel],
+                sampling_rate=eeg_sampling_rate,
+                start_freq=bandpass_low_cutoff_freq,
+                stop_freq=bandpass_high_cutoff_freq,
+                order=bandpass_filter_order,
+                filter_type=FilterTypes.BUTTERWORTH.value,
+                ripple=0.0,  # Ripple is for Chebyshev filters, ignored for Butterworth
+            )
+
+        # ------------------------------------------------------------------------------
+        # *** Truncate EEG data stream by start and end marker
+
+        # The beginning of the stimulus presentation is marked by a start maker (-1.0).
+        # The end is potentially also marked (-2.0). We assume that the marker signal is
+        # in the last channel.
+        marker_channel_data = board_data[marker_channel]
+
+        start_idx = np.where(marker_channel_data == -1.0)[0]
+        if start_idx.size != 0:
+            start_idx = start_idx[0]
+            board_data = board_data[:, start_idx:]
+
+        end_idx = np.where(marker_channel_data == -2.0)[0]
+        if end_idx.size != 0:
+            end_idx = end_idx[0]
+            board_data = board_data[:, :end_idx]
+
+        # TODO: Send auxilliariy data (non-eeg-channels)?
+        eeg_data = board_data[eeg_channels, :]
+
+        # ------------------------------------------------------------------------------
+        # *** Normalize
+
+        eeg_data = zscore(eeg_data, axis=1)
+
+        # ------------------------------------------------------------------------------
+        # *** Truncate data
+
+        print(f"eeg_data: {eeg_data.shape}")
+
+        # TODO: Fix hardcoded time interval.
+        truncated_eeg_data = eeg_data[:, 5:]
+        truncated_eeg_data = truncated_eeg_data[:, :110]
+
+        print(f"truncated_eeg_data: {truncated_eeg_data.shape}")
+
+        # ------------------------------------------------------------------------------
+        # *** Send to remote endpoint
+
+        # TODO: Add the following metadata before sending?
+        # "eeg_board_description": eeg_board_description,
+        # "eeg_sampling_rate": eeg_sampling_rate,
+        # "eeg_channels": eeg_channels,
+        # "eeg_channel_mapping": eeg_channel_mapping,
+
+        payload = {
+            "eeg": truncated_eeg_data.tolist(),
+            "image": "data:image/jpeg;base64," + img_b64,
+            "metadata": metadata,
+        }
+
+        payload = json.dumps(payload)
+
+        response = requests.post(
+            url=nubrain_endpoint,
+            data=payload,
+            headers={"Authorization": f"Bearer {nubrain_api_key}"},
+        )
+
+        if response.status_code != 200:
+            print(
+                f"Failed to send data. Status code: {response.status_code}. "
+                + f"Response: {response.text}"
+            )
+
+        # ------------------------------------------------------------------------------
+        # *** Local data copy
+
+        trial_data = {
+            "stimulus_start_time": metadata["stimulus_start_time"],
+            "stimulus_end_time": metadata["stimulus_end_time"],
+            "stimulus_duration_s": metadata["stimulus_duration_s"],
+            "eeg": eeg_data,
+            "image_filepath": image_filepath,  # TODO image metadata
+        }
+        experiment_data["data"].append(trial_data)
+
+    # ----------------------------------------------------------------------------------
+    # *** Save local data copy
+
+    print("Save data to disk")
+
+    with open(path_out_data, "wb") as file:
+        pickle.dump(experiment_data, file, protocol=pickle.HIGHEST_PROTOCOL)
+
+    # End of data preprocessing process.
+
+
+def experiment(
+    nubrain_api_key: str,
+    eeg_channel_mapping: dict = {
+        0: "O1",  # N1 Cyton pin
+        1: "O2",  # N2 Cyton pin
+        2: "P4",  # N3 Cyton pin
+        3: "P3",  # N4 Cyton pin
+        4: "C4",  # N5 Cyton pin
+        5: "C3",  # N6 Cyton pin
+        6: "F4",  # N7 Cyton pin
+        7: "F3",  # N8 Cyton pin
+    },
+):
+    # ----------------------------------------------------------------------------------
+    # *** Test if path exists
+
+    if not os.path.isdir(output_directory):
+        raise AssertionError(f"Target directory does not exist: {output_directory}")
+
+    current_datetime = get_formatted_current_datetime()
+    path_out_data = os.path.join(
+        output_directory, f"eeg_session_{current_datetime}.pickle"
+    )
+
+    if os.path.isfile(path_out_data):
+        raise AssertionError(f"Target file aready exists: {path_out_data}")
+
+    # ----------------------------------------------------------------------------------
+    # *** Prepare EEG measurement
+
+    BoardShim.enable_dev_board_logger()
+
+    if demo_mode:
+        board_id = BoardIds.SYNTHETIC_BOARD.value
+    else:
+        board_id = BoardIds.CYTON_BOARD.value
+
+    params = BrainFlowInputParams()
+    params.serial_port = "/dev/ttyUSB0"  # ?
+    board = BoardShim(board_id, params)
+
+    eeg_board_description = BoardShim.get_board_descr(board_id)
+    eeg_sampling_rate = int(eeg_board_description["sampling_rate"])
+    eeg_channels = eeg_board_description["eeg_channels"]  # Get EEG channel indices
+    marker_channel = eeg_board_description["marker_channel"]
+
+    board.prepare_session()
+
+    print(f"Board: {eeg_board_description['name']}")
+    print(f"Sampling Rate: {eeg_sampling_rate} Hz")
+    print(f"EEG Channels: {eeg_channels}")
+
+    board.start_stream()
+
+    # ----------------------------------------------------------------------------------
+    # *** Start preprocessing subprocess
+
+    data_to_remote_queue = mp.Queue()
+
+    subprocess_params = {
+        "eeg_board_description": eeg_board_description,
+        "eeg_sampling_rate": eeg_sampling_rate,
+        "eeg_channels": eeg_channels,
+        "eeg_channel_mapping": eeg_channel_mapping,
+        "marker_channel": marker_channel,
+        "bandstop_low_cutoff_freq": bandstop_low_cutoff_freq,
+        "bandstop_high_cutoff_freq": bandstop_high_cutoff_freq,
+        "bandstop_filter_order": bandstop_filter_order,
+        "bandpass_low_cutoff_freq": bandpass_low_cutoff_freq,
+        "bandpass_high_cutoff_freq": bandpass_high_cutoff_freq,
+        "bandpass_filter_order": bandpass_filter_order,
+        "nubrain_endpoint": nubrain_endpoint,
+        "nubrain_api_key": nubrain_api_key,
+        "path_out_data": path_out_data,
+        "data_to_remote_queue": data_to_remote_queue,
+    }
+
+    preprocess_process = mp.Process(
+        target=preprocess,
+        args=(subprocess_params,),
+    )
+
+    preprocess_process.Daemon = True
+    preprocess_process.start()
+
+    # ----------------------------------------------------------------------------------
+    # *** Start experiment
+
+    running = True
+    while running:
+        pygame.init()
+
+        # Get screen dimensions and set up full screen
+        screen_info = pygame.display.Info()
+        screen_width = screen_info.current_w
+        screen_height = screen_info.current_h
+        screen = pygame.display.set_mode(
+            (screen_width, screen_height), pygame.FULLSCREEN
+        )
+        pygame.display.set_caption("Image Presentation Experiment")
+        pygame.mouse.set_visible(False)  # Hide the mouse cursor
+
+        # Load images
+        all_images = load_and_scale_images(
+            image_directory=image_directory,
+            screen_width=screen_width,
+            screen_height=screen_height,
+        )
+
+        if not all_images:
+            print("No images loaded. Exiting.")
+            pygame.quit()
+            break
+
+        font = pygame.font.Font(None, 48)  # Basic font for messages
+
+        try:
+            # 1. Initial grey screen
+            print("Starting initial grey screen...")
+            # sleep(0.1)
+            pygame.time.wait(100)
+            screen.fill(GREY)
+            pygame.display.flip()
+            # sleep(0.1)
+            pygame.time.wait(100)
+            screen.fill(GREY)
+            pygame.display.flip()
+            # sleep(initial_grey_duration)
+            pygame.time.wait(int(round(initial_grey_duration * 100.0)))
+
+            # Block loop.
+            for block_num in range(n_blocks):
+                print(f"\nStarting Block {block_num + 1}/{n_blocks}")
+
+                # Image loop (within a block).
+                for image_count in range(images_per_block):
+                    if not running:
+                        break  # Check for quit event
+
+                    # Select a random image from the full list.
+                    random_sample = random.choice(all_images)
+                    image_filepath = random_sample["image_filepath"]
+                    current_image = random_sample["image"]
+
+                    img_rect = current_image.get_rect(
+                        center=(screen_width // 2, screen_height // 2)
+                    )
+
+                    # Clear board buffer
+                    _ = board.get_board_data()
+
+                    # Display image. Clear previous screen content (optional, good practice).
+                    screen.fill(GREY)
+                    screen.blit(current_image, img_rect)
+                    pygame.display.flip()
+
+                    # Start of stimulus presentation.
+                    t1 = time()
+                    # Insert stimulus start maker into EEG data.
+                    board.insert_marker(stim_start_marker)
+
+                    # Time until when to show stimulus.
+                    t2 = t1 + image_duration
+                    while time() < t2:
+                        pass
+
+                    # End of stimulus presentation. Display ISI grey screen.
+                    screen.fill(GREY)
+                    pygame.display.flip()
+                    board.insert_marker(stim_end_marker)
+                    t3 = time()
+
+                    board_data = (
+                        board.get_board_data()
+                    )  # Gets all data accumulated so far
+
+                    metadata = {
+                        "stimulus_start_time": t1,
+                        "stimulus_end_time": t3,
+                        "stimulus_duration_s": t3 - t1,
+                    }
+
+                    data_to_send = {
+                        "board_data": board_data,
+                        "metadata": metadata,
+                        "image_filepath": image_filepath,
+                    }
+
+                    data_to_remote_queue.put(data_to_send)
+
+                    # Time until when to show grey screen.
+                    t4 = t3 + isi_duration
+                    while time() < t4:
+                        pass
+
+                    # Event handling (allow quitting with ESC or window close).
+                    for event in pygame.event.get():
+                        if event.type == pygame.QUIT:
+                            running = False
+                        if event.type == pygame.KEYDOWN:
+                            if event.key == pygame.K_ESCAPE:
+                                running = False
+
+                    if not running:
+                        break
+
+                if not running:
+                    break
+
+                # 2. Inter-block grey screen (if not the last block)
+                if block_num < n_blocks - 1:
+                    print(
+                        f"End of Block {block_num + 1}. Starting inter-block grey screen..."
+                    )
+                    screen.fill(GREY)
+                    pygame.display.flip()
+                    # sleep(inter_block_grey_duration)
+                    pygame.time.wait(int(round(inter_block_grey_duration * 100.0)))
+                else:
+                    print(f"End of Block {block_num + 1}. Experiment finished.")
+
+            # Final message (optional)
+            if running:  # Only show if not quit early
+                screen.fill(GREY)
+                end_text = font.render("Experiment Complete.", True, BLACK)
+                text_rect = end_text.get_rect(
+                    center=(screen_width // 2, screen_height // 2)
+                )
+                screen.blit(end_text, text_rect)
+                pygame.display.flip()
+                # sleep(0.5)
+                pygame.time.wait(500)
+
+            running = False
+
+        except Exception as e:
+            print(f"An error occurred during the experiment: {e}")
+            running = False
+        finally:
+            pygame.quit()
+            print("Experiment closed.")
+
+    board.stop_stream()
+    board.release_session()
+
+    # Join process for sending data.
+    print("Join process for sending data")
+    data_to_remote_queue.put(None)
+    preprocess_process.join()

nubrain-0.0.0/pyproject.toml

@@ -0,0 +1,32 @@
+[project]
+name = "nubrain"
+version = "0.0.0"
+description = "NuBrain connect"
+authors = [{ name = "nuBrain Team", email = "hello@nubrain.io" }]
+requires-python = ">=3.10"
+readme = "README.md"
+dependencies = [
+    "brainflow>=5.16.0",
+    "certifi>=2025.4.26",
+    "charset-normalizer>=3.4.2",
+    "idna>=3.10",
+    "numpy>=2.2.6",
+    "pillow>=11.2.1",
+    "pygame>=2.6.1",
+    "requests>=2.32.3",
+    "scipy>=1.15.3",
+    "setuptools>=80.9.0",
+    "urllib3>=2.4.0",
+]
+license = "MIT"
+license-files = ["LICENSE"]
+
+[build-system]
+requires = ["hatchling >= 1.26"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.wheel]
+packages = ["nubrain"]
+
+[project.urls]
+Homepage = "https://github.com/ingo-m/nubrain-connect"

nubrain-0.0.0/uv.lock

@@ -0,0 +1,462 @@
+version = 1
+revision = 2
+requires-python = ">=3.10"
+resolution-markers = [
+    "python_full_version >= '3.11'",
+    "python_full_version < '3.11'",
+]
+
+[[package]]
+name = "brainflow"
+version = "5.18.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "numpy", version = "2.2.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" },
+    { name = "numpy", version = "2.3.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" },
+    { name = "setuptools" },
+]
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/61/c2/b9b80a1c7c5d3d682163bf8863e57f44c77be8b32887c8bd6877c2dae850/brainflow-5.18.0-py3-none-any.whl", hash = "sha256:70d249ab9e8622d5775cba816fe89cf6be71e5250bdbb392e732d8d6688a42cc", size = 30979354, upload-time = "2025-05-31T21:31:06.13Z" },
+]
+
+[[package]]
+name = "certifi"
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