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Merge pull request #3 from catalystneuro/add_time_synch
Add time synch for Fox lab
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,207 @@ | ||
| from lxml import etree | ||
| import os | ||
|
|
||
| def extract_phantom_metadata(xml_path): | ||
| # Parse XML using lxml | ||
| tree = etree.parse(xml_path) | ||
| root = tree.getroot() | ||
|
|
||
| # Create metadata dictionary | ||
| metadata = {} | ||
|
|
||
| # Define paths and their corresponding keys/types | ||
| paths = { | ||
| # Camera settings | ||
| "frame_rate": (".//FrameRateDouble", float), | ||
| "total_frames": (".//TotalImageCount", int), | ||
| "first_frame": (".//FirstMovieImage", int), | ||
| "image_count": (".//ImageCount", int), | ||
| # Image properties | ||
| "width": (".//biWidth", int), | ||
| "height": (".//biHeight", int), | ||
| "bit_depth": (".//biBitCount", int), | ||
| "bit_depth_recording": (".//RecBPP", int), | ||
| # Camera info | ||
| "camera_model": (".//CameraModel", str), | ||
| "camera_version": (".//CameraVersion", int), | ||
| "firmware_version": (".//FirmwareVersion", int), | ||
| "software_version": (".//SoftwareVersion", int), | ||
| "serial": (".//Serial", int), | ||
| # Timing | ||
| "shutter_ns": (".//ShutterNs", int), | ||
| "frame_delay_ns": (".//FrameDelayNs", int), | ||
| # Image settings | ||
| "compression": (".//Compression", int), | ||
| "saturation": (".//Saturation", float), | ||
| "brightness": (".//Bright", int), | ||
| "contrast": (".//Contrast", int), | ||
| "gamma": (".//Gamma", float), | ||
| # Trigger settings | ||
| "trigger_frame": (".//TrigFrame", int), | ||
| "post_trigger": (".//PostTrigger", int), | ||
| # Auto exposure | ||
| "auto_exposure": (".//AutoExposure", bool), | ||
| "auto_exp_level": (".//AutoExpLevel", int), | ||
| "auto_exp_speed": (".//AutoExpSpeed", int), | ||
| } | ||
|
|
||
| # Extract all metadata based on paths | ||
| for key, (xpath, type_conv) in paths.items(): | ||
| element = root.find(xpath) | ||
| if element is not None and element.text: | ||
| try: | ||
| metadata[key] = type_conv(element.text) | ||
| except (ValueError, TypeError): | ||
| metadata[key] = None | ||
| else: | ||
| metadata[key] = None | ||
|
|
||
| # Special handling for trigger time | ||
| trigger_date = root.find(".//TriggerTime/Date") | ||
| trigger_time = root.find(".//TriggerTime/Time") | ||
| if trigger_date is not None and trigger_time is not None: | ||
| metadata["trigger_time"] = f"{trigger_date.text} {trigger_time.text}" | ||
|
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||
| # Get image acquisition position and size | ||
| metadata["acquisition"] = { | ||
| "pos_x": int(root.find(".//ImPosXAcq").text) if root.find(".//ImPosXAcq") is not None else None, | ||
| "pos_y": int(root.find(".//ImPosYAcq").text) if root.find(".//ImPosYAcq") is not None else None, | ||
| "width": int(root.find(".//ImWidthAcq").text) if root.find(".//ImWidthAcq") is not None else None, | ||
| "height": int(root.find(".//ImHeightAcq").text) if root.find(".//ImHeightAcq") is not None else None, | ||
| } | ||
|
|
||
| # Get white balance gains | ||
| wb_element = root.find(".//WBGain") | ||
| if wb_element is not None: | ||
| metadata["white_balance"] = { | ||
| "red": float(wb_element.find("Red").text) if wb_element.find("Red") is not None else None, | ||
| "blue": float(wb_element.find("Blue").text) if wb_element.find("Blue") is not None else None, | ||
| } | ||
|
|
||
| return metadata | ||
|
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||
|
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| from typing import Any | ||
|
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||
|
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| def extract_fastec_metadata(file_path: str) -> dict[str, dict[str, Any]]: | ||
| """ | ||
| Extract metadata from a Fastec camera metadata file. | ||
| Parameters | ||
| ---------- | ||
| file_path : str | ||
| Path to the Fastec metadata file. | ||
| Returns | ||
| ------- | ||
| Dict[str, Dict[str, Any]] | ||
| Nested dictionary containing the parsed metadata. | ||
| The top level dictionary has sections as keys ('image', 'camera', 'record', 'normalization'). | ||
| Each section contains a dictionary of key-value pairs with automatically converted data types. | ||
| Notes | ||
| ----- | ||
| The function automatically converts values to appropriate types: | ||
| - Integers for numeric values | ||
| - Floats for decimal numbers | ||
| - Lists for matrix values [x,y,z] | ||
| - Tuples for bit modes (e.g., "10:3") | ||
| - Strings for text and other values | ||
| Examples | ||
| -------- | ||
| >>> metadata = extract_fastec_metadata('metadata.txt') | ||
| >>> frame_rate = metadata['record']['fps'] | ||
| >>> resolution = (metadata['image']['width'], metadata['image']['height']) | ||
| Raises | ||
| ------ | ||
| FileNotFoundError | ||
| If the metadata file is not found. | ||
| PermissionError | ||
| If there are insufficient permissions to read the file. | ||
| """ | ||
|
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||
| def parse_value(value: str) -> int | float | list[int] | tuple[int, int] | str: | ||
| """ | ||
| Parse a string value into its appropriate type. | ||
| Parameters | ||
| ---------- | ||
| value : str | ||
| The string value to parse | ||
| Returns | ||
| ------- | ||
| int | float | list[int] | tuple[int, int] | str | ||
| Parsed value in its appropriate type | ||
| """ | ||
| # Try to convert to int | ||
| try: | ||
| return int(value) | ||
| except ValueError: | ||
| pass | ||
|
|
||
| # Try to convert to float | ||
| try: | ||
| return float(value) | ||
| except ValueError: | ||
| pass | ||
|
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| # Handle matrix values [x,y,z] | ||
| if value.startswith("[") and value.endswith("]"): | ||
| try: | ||
| return [int(x) for x in value[1:-1].split(",")] | ||
| except ValueError: | ||
| return value | ||
|
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| # Handle bit mode (e.g., "10:3") | ||
| if ":" in value and len(value.split(":")) == 2: | ||
| try: | ||
| return tuple(int(x) for x in value.split(":")) | ||
| except ValueError: | ||
| return value | ||
|
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| # Return as string if no other type matches | ||
| return value | ||
|
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| # Check if file exists | ||
| if not os.path.exists(file_path): | ||
| raise FileNotFoundError(f"Metadata file not found: {file_path}") | ||
|
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| metadata: Dict[str, Dict[str, Any]] = {} | ||
| current_section: Union[str, None] = None | ||
|
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| try: | ||
| with open(file_path, "r") as file: | ||
| for line in file: | ||
| line = line.strip() | ||
|
|
||
| # Skip empty lines | ||
| if not line: | ||
| continue | ||
|
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| # Check if line is a section header | ||
| if line.startswith("[") and line.endswith("]"): | ||
| current_section = line[1:-1].lower() | ||
| metadata[current_section] = {} | ||
| continue | ||
|
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||
| # Parse key-value pairs | ||
| if "=" in line and current_section is not None: | ||
| key, value = line.split("=", 1) | ||
| key = key.strip() | ||
| value = value.strip() | ||
|
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| # Parse value to appropriate type | ||
| parsed_value = parse_value(value) | ||
|
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| metadata[current_section][key] = parsed_value | ||
|
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| return metadata | ||
|
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| except PermissionError: | ||
| raise PermissionError(f"Insufficient permissions to read file: {file_path}") | ||
| except Exception as e: | ||
| raise Exception(f"Error parsing metadata file: {str(e)}") |
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