matchypatchy 0.2.1__tar.gz

matchypatchy-0.2.1/LICENSE

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+MIT License
+
+Copyright (c) 2024 Conservation Technology Lab
+
+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.

matchypatchy-0.2.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: matchypatchy
+Version: 0.2.1
+Summary: GUI tool for human validation of AI-powered animal re-identification
+Author-email: Kyra Swanson <tswanson@sdzwa.org>
+Project-URL: Homepage, https://github.com/onservationtechlab/matchypatchy
+Project-URL: Issues, https://github.com/onservationtechlab/matchypatchy/issues
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: animl-lite==3.3.2
+Requires-Dist: chromadb>=1.3.4
+Requires-Dist: pyqt6>=6.9.0
+Dynamic: license-file
+
+# MatchyPatchy
+<br/>
+
+[User Manual](https://conservationtechlab.github.io/matchypatchy/)
+
+MatchyPatchy is an open-source GUI tool for human validation of AI-powered animal re-identification.\
+It was developed by the San Diego Zoo Wildlife Alliance Conservation Technology Lab.\
+Author: Kyra Swanson, (c) 2025
+<br/>
+
+---
+## Installation
+
+Matchypatchy is a stand-alone executable built in Python. Download it [here](). \
+[Github Repository](https://github.com/conservationtechlab/matchypatchy)
+<br/>
+
+---
+## Getting Started
+<br/>
+
+### Download Models
+In order to calculate potential matches, MatchyPatchy requires an animal object detector such as [MegaDetector]()
+and an embedding extractor such as [MiewID]().  Both models and more can be obtained from the SDZWA server by selecting 
+'Download Models' and checking the box associated with which models you want to download.
+<br/>
+
+### Select Survey
+In order to add media to the database, you must first specify a Survey using 
+the dropdown of available surveys. To add a new survey, 
+
+1. Select 'Manage Surveys'
+2. Select 'New' 
+3. Enter Survey Name
+4. Enter Survey Region
+5. (Optional) Enter Survey Start Year
+6. (Optional) Enter Survey End Year
+7. Select 'Ok'
+<br/>
+
+### 1. Import Images
+Images can be imported via spreadsheet or by manually selecting a directory of images.
+
+**From CSV**
+1. Select '1. Import from CSV'
+2. Open .csv file
+3. Select column headers that correspond to image Filepath, Timestamp, Survey, and Station
+4. Optionally select column headers that correspond to image Region, Sequence ID, External ID,
+    Viewpoint, Species, Individual ID, and Comment
+5. Select 'Ok'
+<br/>
+
+**From Folder**
+1. Select '1. Import from Folder'
+2. Open directory containing image files. Can be a whole Survey containg multiple Stations or single Station.
+3. Select the directory level that corresponds to Station name if available
+4. Select 'Ok'
+<br/>
+
+### 2. Process Images
+Run images through a sequence of AI models to obtain predicted matches.\
+Note: Models must be accessible in MatchyPatchy's "Models" folder - see Configuration for more.
+
+1. Select '2. Process'
+2. (Optional) Check Calculate Sequence (improves performance for videos and images captured in quick succession)
+3. **Select Detector Model** - recommended MegaDetector v5a
+4. (Optional) Select Species Classifier Model
+5. **Select Re-Indentification Model** - required to obtain predicted matches, recommended MiewIDv3
+6. (Optional) Select Viewpoint Model (improves performance by estimating animal viewpoint and limiting search space)
+<br/>
+
+### 3. Validate 
+After processing, this pageview allows you to review the imported media for errors, make changes, delete images, etc.
+It can be accessed at any time after image import. 
+<br/>
+
+Double-clicking on a cell will allow you to edit it.\
+Double-clicking on a single row will pull up a screen to edit multiple fields for an image.\
+Selecting one or more row (either by clicking on the row number or checking the select box) will enable the ability
+to mass edit particular fields, duplicate entries, or delete entries.
+<br/>
+
+The **"Show"** Option allows you view the full images or detected ROIS.\
+The **"Save"** Option saves all edits to the database.\
+The **"Undo"** Option undoes the last edit made.
+<br/>
+
+**Filters** \
+Images can be filtered by Region, Survey, Station, Species, and Individual.\
+You can also choose to show only "Unidentified" ROIs.\
+You can also display all images marked as "Favorite"
+<br/>
+
+### 4. Match
+After processing, potential matches can be validated at this pageview.
+The left side contains a **Query** image and the right side contains potential **Matches**.
+If "Calculate Sequence" was selected during the processing stage, the entire **Sequence** will be viewable on the Query side.
+The pageview will display the images and associated metadata. 
+<br/>
+
+_View Options_\
+Adjustments can be made to the **Maximum Number of Matches** shown for each image (within a sequence) and to the maximum distance
+threshold between the two images to qualify as a match. The **Cosine** or **L2** distance of the Match from the Query is displayed above the 
+match image. Select which distance metric to use in the dropdown. You must select **"Recalculate Matches"** if changes are made to either option
+in order to display those changes.\
+After matches are validated, you can **"Query by Individual"** to do quality control and ensure all images associated with
+an individual are indeed valid.\
+Images can be **Filtered** by Region, Survey, or Station to narrow the available matches shown.\
+If **"Viewpoint"** was calculated at the processing step, you can filter both the **Query** and the **Match** images by Viewpoint.\
+The **"View Data"** Button at the bottom brings you to the Media Validation pageview. 
+<br/>
+
+_Image Options_\
+You can adjust the **Brightness, Contrast** and **Sharpness** of each image, as well as **Zoom** using the mouse scroll wheel.\
+The **"Reset"** button returns the image to its original form.\
+The **"Edit Image"** option allows you to make changes to the metadata.\
+The **"Open Image"** option opens the image in your default image viewer.\
+The **"♥"** option marks the image with the "Favorite" tag.
+<br/>
+
+To confirm a match between the Query and the Match image, select the **"Match" button** in the middle, or press the 'M' or 'Space Key'.
+Pressing Match again will undo the match, asking you to confirm first.\
+You can navigate between Query Sequences and Matches by using the **"<<"** and **">>"** buttons, or by using the arrow keys.\
+You can also toggle the **Viewpoint** by pressing 'V'.
+<br/>
+
+### 5. Export
+The database can be exported as a .csv file. Simply select '5. Export' and specify the file name and location. 
+<br/>
+
+---
+## Database Management
+<br/>
+
+### Definitions
+* Survey - An ecological study employing camera traps to investigate wildlife of a particular area.
+* Region - A geographical region that may host one or more camera trap surveys.
+* Station - Reference to a physical location containing one or camera traps.
+* Species - The taxonomic and common names refering to a class of animal.
+* Media - Image (and soon video) files obtained from camera traps.
+* ROI - Regions of Interest within media files that contain animals. 
+* Individual - A particular, singular example of a given species, can be named/ID'd.
+* Sequence ID - A unique number associated with a set of sequential images or frames in a video.
+* External ID - A unique number used to reference MatchyPatchy output with other datamanagement tools.
+* Viewpoint - The side of the body of the animl facing the camera, eg "Left", "Right", "Top"
+* Comment - Notes or concerns about a particular media file
+* Favorite - A tag marking an image as noteworthy.
+<br/>
+
+### Manage Tables
+**Survey, Station,** and **Species** tables can be managed independently. 
+<br/>
+
+### CSV Import
+<br/>
+
+
+---
+## Configuration
+<br/>
+
+### Available Models
+Models currently available and compatible with MatchyPatchy:\
+_Detector Models_:
+- MegaDetector v5a
+- MegaDetector v5b
+
+_Re-ID Models_: 
+- MiewID v3
+- MiewID v2
+
+_Viewpoint Models_:
+- SDZWA Viewpoint
+<br/>
+
+### Link to New Database
+Database files can be shared across multiple users of MatchyPatchy. To link to a new .db file, 
+<br/>
+
+### Clear Data 

matchypatchy-0.2.1/README.md

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+# MatchyPatchy
+<br/>
+
+[User Manual](https://conservationtechlab.github.io/matchypatchy/)
+
+MatchyPatchy is an open-source GUI tool for human validation of AI-powered animal re-identification.\
+It was developed by the San Diego Zoo Wildlife Alliance Conservation Technology Lab.\
+Author: Kyra Swanson, (c) 2025
+<br/>
+
+---
+## Installation
+
+Matchypatchy is a stand-alone executable built in Python. Download it [here](). \
+[Github Repository](https://github.com/conservationtechlab/matchypatchy)
+<br/>
+
+---
+## Getting Started
+<br/>
+
+### Download Models
+In order to calculate potential matches, MatchyPatchy requires an animal object detector such as [MegaDetector]()
+and an embedding extractor such as [MiewID]().  Both models and more can be obtained from the SDZWA server by selecting 
+'Download Models' and checking the box associated with which models you want to download.
+<br/>
+
+### Select Survey
+In order to add media to the database, you must first specify a Survey using 
+the dropdown of available surveys. To add a new survey, 
+
+1. Select 'Manage Surveys'
+2. Select 'New' 
+3. Enter Survey Name
+4. Enter Survey Region
+5. (Optional) Enter Survey Start Year
+6. (Optional) Enter Survey End Year
+7. Select 'Ok'
+<br/>
+
+### 1. Import Images
+Images can be imported via spreadsheet or by manually selecting a directory of images.
+
+**From CSV**
+1. Select '1. Import from CSV'
+2. Open .csv file
+3. Select column headers that correspond to image Filepath, Timestamp, Survey, and Station
+4. Optionally select column headers that correspond to image Region, Sequence ID, External ID,
+    Viewpoint, Species, Individual ID, and Comment
+5. Select 'Ok'
+<br/>
+
+**From Folder**
+1. Select '1. Import from Folder'
+2. Open directory containing image files. Can be a whole Survey containg multiple Stations or single Station.
+3. Select the directory level that corresponds to Station name if available
+4. Select 'Ok'
+<br/>
+
+### 2. Process Images
+Run images through a sequence of AI models to obtain predicted matches.\
+Note: Models must be accessible in MatchyPatchy's "Models" folder - see Configuration for more.
+
+1. Select '2. Process'
+2. (Optional) Check Calculate Sequence (improves performance for videos and images captured in quick succession)
+3. **Select Detector Model** - recommended MegaDetector v5a
+4. (Optional) Select Species Classifier Model
+5. **Select Re-Indentification Model** - required to obtain predicted matches, recommended MiewIDv3
+6. (Optional) Select Viewpoint Model (improves performance by estimating animal viewpoint and limiting search space)
+<br/>
+
+### 3. Validate 
+After processing, this pageview allows you to review the imported media for errors, make changes, delete images, etc.
+It can be accessed at any time after image import. 
+<br/>
+
+Double-clicking on a cell will allow you to edit it.\
+Double-clicking on a single row will pull up a screen to edit multiple fields for an image.\
+Selecting one or more row (either by clicking on the row number or checking the select box) will enable the ability
+to mass edit particular fields, duplicate entries, or delete entries.
+<br/>
+
+The **"Show"** Option allows you view the full images or detected ROIS.\
+The **"Save"** Option saves all edits to the database.\
+The **"Undo"** Option undoes the last edit made.
+<br/>
+
+**Filters** \
+Images can be filtered by Region, Survey, Station, Species, and Individual.\
+You can also choose to show only "Unidentified" ROIs.\
+You can also display all images marked as "Favorite"
+<br/>
+
+### 4. Match
+After processing, potential matches can be validated at this pageview.
+The left side contains a **Query** image and the right side contains potential **Matches**.
+If "Calculate Sequence" was selected during the processing stage, the entire **Sequence** will be viewable on the Query side.
+The pageview will display the images and associated metadata. 
+<br/>
+
+_View Options_\
+Adjustments can be made to the **Maximum Number of Matches** shown for each image (within a sequence) and to the maximum distance
+threshold between the two images to qualify as a match. The **Cosine** or **L2** distance of the Match from the Query is displayed above the 
+match image. Select which distance metric to use in the dropdown. You must select **"Recalculate Matches"** if changes are made to either option
+in order to display those changes.\
+After matches are validated, you can **"Query by Individual"** to do quality control and ensure all images associated with
+an individual are indeed valid.\
+Images can be **Filtered** by Region, Survey, or Station to narrow the available matches shown.\
+If **"Viewpoint"** was calculated at the processing step, you can filter both the **Query** and the **Match** images by Viewpoint.\
+The **"View Data"** Button at the bottom brings you to the Media Validation pageview. 
+<br/>
+
+_Image Options_\
+You can adjust the **Brightness, Contrast** and **Sharpness** of each image, as well as **Zoom** using the mouse scroll wheel.\
+The **"Reset"** button returns the image to its original form.\
+The **"Edit Image"** option allows you to make changes to the metadata.\
+The **"Open Image"** option opens the image in your default image viewer.\
+The **"♥"** option marks the image with the "Favorite" tag.
+<br/>
+
+To confirm a match between the Query and the Match image, select the **"Match" button** in the middle, or press the 'M' or 'Space Key'.
+Pressing Match again will undo the match, asking you to confirm first.\
+You can navigate between Query Sequences and Matches by using the **"<<"** and **">>"** buttons, or by using the arrow keys.\
+You can also toggle the **Viewpoint** by pressing 'V'.
+<br/>
+
+### 5. Export
+The database can be exported as a .csv file. Simply select '5. Export' and specify the file name and location. 
+<br/>
+
+---
+## Database Management
+<br/>
+
+### Definitions
+* Survey - An ecological study employing camera traps to investigate wildlife of a particular area.
+* Region - A geographical region that may host one or more camera trap surveys.
+* Station - Reference to a physical location containing one or camera traps.
+* Species - The taxonomic and common names refering to a class of animal.
+* Media - Image (and soon video) files obtained from camera traps.
+* ROI - Regions of Interest within media files that contain animals. 
+* Individual - A particular, singular example of a given species, can be named/ID'd.
+* Sequence ID - A unique number associated with a set of sequential images or frames in a video.
+* External ID - A unique number used to reference MatchyPatchy output with other datamanagement tools.
+* Viewpoint - The side of the body of the animl facing the camera, eg "Left", "Right", "Top"
+* Comment - Notes or concerns about a particular media file
+* Favorite - A tag marking an image as noteworthy.
+<br/>
+
+### Manage Tables
+**Survey, Station,** and **Species** tables can be managed independently. 
+<br/>
+
+### CSV Import
+<br/>
+
+
+---
+## Configuration
+<br/>
+
+### Available Models
+Models currently available and compatible with MatchyPatchy:\
+_Detector Models_:
+- MegaDetector v5a
+- MegaDetector v5b
+
+_Re-ID Models_: 
+- MiewID v3
+- MiewID v2
+
+_Viewpoint Models_:
+- SDZWA Viewpoint
+<br/>
+
+### Link to New Database
+Database files can be shared across multiple users of MatchyPatchy. To link to a new .db file, 
+<br/>
+
+### Clear Data 

matchypatchy-0.2.1/pyproject.toml

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+[project]
+name = "matchypatchy"
+dynamic = ["version"]
+authors = [
+  { name="Kyra Swanson", email="tswanson@sdzwa.org" },
+]
+description = "GUI tool for human validation of AI-powered animal re-identification"
+readme = "README.md"
+requires-python = ">=3.12"
+dependencies = [
+    "animl-lite==3.3.2",
+    "chromadb>=1.3.4",
+    "pyqt6>=6.9.0",
+]
+
+[project.urls]
+Homepage = "https://github.com/onservationtechlab/matchypatchy"
+Issues = "https://github.com/onservationtechlab/matchypatchy/issues"
+
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.dynamic]
+version = {attr = "matchypatchy.__version__"}
+
+[tool.setuptools]
+packages = ["matchypatchy"]
+package-dir = {"" = "src"}
+ 
+[tool.setuptools.package-data]
+matchypatchy = ["assets/**/*", "assets/graphics/*"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "-v"
+
+[tool.pylint.master]
+extension-pkg-whitelist = ["PyQt6"]
+
+[tool.pylint.messages_control]
+disable = ["no-name-in-module"]

matchypatchy-0.2.1/setup.cfg

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

matchypatchy-0.2.1/src/matchypatchy/__init__.py

@@ -0,0 +1,105 @@
+__version__ = "0.2.1"
+
+from matchypatchy import config
+from matchypatchy import database
+from matchypatchy import gui
+from matchypatchy import logging_config
+from matchypatchy import threads
+
+from matchypatchy.config import (asset_path, mpConfig, resource_path,)
+from matchypatchy.database import (EditObject, IMAGE_EXT, MatchyPatchyDB,
+                                   THUMBNAIL_NOTFOUND, THUMBNAIL_SIZE,
+                                   TZ_CONVERT_DICT, VIDEO_EXT,
+                                   check_missing_thumbnails, fetch_individual,
+                                   fetch_media, fetch_media_thumbnails,
+                                   fetch_regions, fetch_roi, fetch_roi_media,
+                                   fetch_roi_thumbnails,
+                                   fetch_station_names_from_id, fetch_stations,
+                                   fetch_surveys, get_frame, get_roi_bbox,
+                                   get_sequence, get_sha256,
+                                   individual_roi_dict, location, media,
+                                   media_count, mpdb, save_media_thumbnail,
+                                   save_roi_thumbnail, sequence_roi_dict,
+                                   setup, setup_chromadb, setup_database,
+                                   thumbnails,)
+from matchypatchy.gui import (AlertPopup, ClickableSlider, ComboBoxDelegate,
+                              ComboBoxSeparator, ConfigPopup, DisplayBase,
+                              DisplayCompare, DisplayMedia, FilterBar,
+                              FilterBox, HorizontalSeparator, ImageAdjustBar,
+                              ImageWidget, ImportCSVPopup, ImportFolderPopup,
+                              IndividualFillPopup, IndividualPopup,
+                              MLDownloadPopup, MLOptionsPopup, MainWindow,
+                              ManualQueryContainer, MediaEditPopup, MediaTable,
+                              MediaWidget, MetadataPanel, NoHoverDelegate,
+                              PairXPopup, QC_QueryContainer, QueryContainer,
+                              READMEPopup, SequenceSelector, SliderWithLabel,
+                              StandardButton, StationFillPopup, StationPopup,
+                              SurveyFillPopup, SurveyPopup, TextEditWithSignal,
+                              ThreePointSlider, UploadManagerPopup,
+                              VerticalSeparator, VideoPlayerBar, VideoViewer,
+                              VideoWidget, dialogs, display_base,
+                              display_compare, display_media, gui_assets,
+                              main_gui, manual_query, media_table, popup_alert,
+                              popup_config, popup_import_csv,
+                              popup_import_folder, popup_individual,
+                              popup_media_edit, popup_ml, popup_pairx,
+                              popup_readme, popup_station, popup_survey,
+                              popup_uploads, qc_query, query, widget_filterbar,
+                              widget_image_adjustment, widget_media, widgets,)
+from matchypatchy.logging_config import (get_logger, setup_logger,)
+from matchypatchy.threads import (AnimlThread, BasePathUpdateThread,
+                                  BuildManifestThread, CSVImportThread,
+                                  CSVMigrateThread, DownloadMLThread,
+                                  FavoriteMatchObject, FetchTableThread,
+                                  FolderImportThread, MEGADETECTORv1000_SIZE,
+                                  MatchEmbeddingThread, MatchObject,
+                                  ReIDThread, SequenceThread,
+                                  VerifyNewBaseDirsThread, animl_thread,
+                                  delete, get_path, import_thread,
+                                  is_valid_reid_model, load_model,
+                                  match_object, match_thread,
+                                  model_download_thread, reid_thread,
+                                  sequence_thread, table_thread,
+                                  update_model_yml,)
+
+__all__ = ['AlertPopup', 'AnimlThread', 'BasePathUpdateThread',
+           'BuildManifestThread', 'CSVImportThread', 'CSVMigrateThread',
+           'ClickableSlider', 'ComboBoxDelegate', 'ComboBoxSeparator',
+           'ConfigPopup', 'DisplayBase', 'DisplayCompare', 'DisplayMedia',
+           'DownloadMLThread', 'EditObject', 'FavoriteMatchObject',
+           'FetchTableThread', 'FilterBar', 'FilterBox', 'FolderImportThread',
+           'HorizontalSeparator', 'IMAGE_EXT', 'ImageAdjustBar', 'ImageWidget',
+           'ImportCSVPopup', 'ImportFolderPopup', 'IndividualFillPopup',
+           'IndividualPopup', 'MEGADETECTORv1000_SIZE', 'MLDownloadPopup',
+           'MLOptionsPopup', 'MainWindow', 'ManualQueryContainer',
+           'MatchEmbeddingThread', 'MatchObject', 'MatchyPatchyDB',
+           'MediaEditPopup', 'MediaTable', 'MediaWidget', 'MetadataPanel',
+           'NoHoverDelegate', 'PairXPopup', 'QC_QueryContainer',
+           'QueryContainer', 'READMEPopup', 'ReIDThread', 'SequenceSelector',
+           'SequenceThread', 'SliderWithLabel', 'StandardButton',
+           'StationFillPopup', 'StationPopup', 'SurveyFillPopup',
+           'SurveyPopup', 'THUMBNAIL_NOTFOUND', 'THUMBNAIL_SIZE',
+           'TZ_CONVERT_DICT', 'TextEditWithSignal', 'ThreePointSlider',
+           'UploadManagerPopup', 'VIDEO_EXT', 'VerifyNewBaseDirsThread',
+           'VerticalSeparator', 'VideoPlayerBar', 'VideoViewer', 'VideoWidget',
+           'animl_thread', 'asset_path', 'check_missing_thumbnails', 'config',
+           'database', 'delete', 'dialogs', 'display_base', 'display_compare',
+           'display_media', 'fetch_individual', 'fetch_media',
+           'fetch_media_thumbnails', 'fetch_regions', 'fetch_roi',
+           'fetch_roi_media', 'fetch_roi_thumbnails',
+           'fetch_station_names_from_id', 'fetch_stations', 'fetch_surveys',
+           'get_frame', 'get_logger', 'get_path', 'get_roi_bbox',
+           'get_sequence', 'get_sha256', 'gui', 'gui_assets', 'import_thread',
+           'individual_roi_dict', 'is_valid_reid_model', 'load_model',
+           'location', 'logging_config', 'main_gui', 'manual_query',
+           'match_object', 'match_thread', 'media', 'media_count',
+           'media_table', 'model_download_thread', 'mpConfig', 'mpdb',
+           'popup_alert', 'popup_config', 'popup_import_csv',
+           'popup_import_folder', 'popup_individual', 'popup_media_edit',
+           'popup_ml', 'popup_pairx', 'popup_readme', 'popup_station',
+           'popup_survey', 'popup_uploads', 'qc_query', 'query', 'reid_thread',
+           'resource_path', 'save_media_thumbnail', 'save_roi_thumbnail',
+           'sequence_roi_dict', 'sequence_thread', 'setup', 'setup_chromadb',
+           'setup_database', 'setup_logger', 'table_thread', 'threads',
+           'thumbnails', 'update_model_yml', 'widget_filterbar',
+           'widget_image_adjustment', 'widget_media', 'widgets']

matchypatchy-0.2.1/src/matchypatchy/__main__.py

@@ -0,0 +1,78 @@
+'''
+Main entry point for MatchyPatchy application
+'''
+
+import os
+import sys
+import time
+from pathlib import Path
+from PyQt6.QtWidgets import QApplication
+
+from matchypatchy.logging_config import setup_logger, get_logger
+from matchypatchy.gui import MainWindow
+
+
+def setup_cuda_path():
+    """Dynamically find and add NVIDIA CUDA/cuDNN libraries to PATH"""
+    try:
+        # Try to find nvidia packages in site-packages
+        import site
+        site_packages = site.getsitepackages()
+        
+        if isinstance(site_packages, str):
+            site_packages = [site_packages]
+        
+        for site_dir in site_packages:
+            nvidia_lib_path = Path(site_dir) / "nvidia"
+            
+            if nvidia_lib_path.exists():
+                dll_folders = [
+                    nvidia_lib_path / "cuda_runtime" / "bin",
+                    nvidia_lib_path / "cuda_nvrtc" / "bin",
+                    nvidia_lib_path / "cublas" / "bin",
+                    nvidia_lib_path / "cudnn" / "bin",
+                ]
+                
+                for folder in dll_folders:
+                    if folder.exists():
+                        os.environ['PATH'] = str(folder) + os.pathsep + os.environ['PATH']
+                
+                return True
+    except Exception as e:
+        print(f"Warning: Could not setup CUDA path: {e}")
+    
+    return False
+
+
+if __name__ == "__main__":
+    start_time = time.time()
+    
+    # Setup application-wide logging
+    root_logger = setup_logger()
+    logger = get_logger(__name__)
+    logger.info("=" * 70)
+    logger.info("MatchyPatchy starting up...")
+
+    exit_code = 1  # Default to error; overwritten on successful run
+
+    try:
+        setup_cuda_path()
+        app = QApplication(sys.argv)
+        window = MainWindow(logger)
+        logger.info("Main window initialized")
+        window.show()
+        
+        startup_time = time.time() - start_time
+        logger.info(f"Startup took {startup_time:.2f} seconds")
+        logger.info("-" * 70)
+        
+        exit_code = app.exec()
+
+    except Exception as e:
+        logger.error(f"Fatal error during startup: {e}", exc_info=True)
+        exit_code = 1
+    
+    finally:
+        logger.info("MatchyPatchy shutting down")
+        logger.info("=" * 70)
+        sys.exit(exit_code)

matchypatchy-0.2.1/src/matchypatchy/assets/models.yml

@@ -0,0 +1,25 @@
+MODELS: 
+  "MegaDetector": 
+    - ["md_v1000.0.0-sorrel.onnx"]
+    - ["https://sandiegozoo.box.com/shared/static/7z9xagk8zweu6op3dgdk386jf9ayl2gt.onnx"]
+  "miewid_v3": 
+    - ["miewid_v3.onnx", "miewid_v3.onnx.data"]
+    - ["https://sandiegozoo.box.com/shared/static/ppm0odjgscvpj9lf5ax86p3fqu5vraxw.onnx",
+       "https://sandiegozoo.box.com/shared/static/xi1dijx35ta2tqtu2sa28bd09ve9li6f.data"]
+  "Jaguar Viewpoint": 
+    - ["sdzwa_jaguar_viewpoint.onnx", "sdzwa_jaguar_viewpoint.onnx.data"]
+    - ["https://sandiegozoo.box.com/shared/static/nkuku5aeicg9hugo0hogdjxg667xodlb.onnx",
+       "https://sandiegozoo.box.com/shared/static/3563emet6b6tubtgtqce8144dlq3z8y5.data"]
+
+
+DETECTOR_MODELS: 
+  - "MegaDetector"
+
+REID_MODELS: ["miewid_v3"]
+VIEWPOINT_MODELS: ["Jaguar Viewpoint"]
+
+VIEWPOINTS:
+  'Any': "Any"
+  'None': "None"
+  '0': "Right"
+  '1': "Left"

matchypatchy-0.2.1/src/matchypatchy/assets/schema.txt

@@ -0,0 +1,106 @@
+TABLE: metadata
+CREATE TABLE metadata (
+                id INTEGER PRIMARY KEY,
+                mp_version TEXT NOT NULL,
+                key TEXT UNIQUE NOT NULL )
+INDEX: sqlite_autoindex_metadata_1
+None
+TABLE: region
+CREATE TABLE region (
+                id INTEGER PRIMARY KEY,
+                name TEXT UNIQUE NOT NULL, 
+                timezone TEXT)
+INDEX: sqlite_autoindex_region_1
+None
+TABLE: survey
+CREATE TABLE survey (
+                id INTEGER PRIMARY KEY,
+                name TEXT UNIQUE NOT NULL,
+                region_id INTEGER,
+                year_start INTEGER,
+                year_end INTEGER,
+                FOREIGN KEY (region_id) REFERENCES region (id) ON DELETE SET NULL)
+INDEX: sqlite_autoindex_survey_1
+None
+TABLE: station
+CREATE TABLE station (
+                id INTEGER PRIMARY KEY,
+                name TEXT NOT NULL,
+                lat REAL,
+                long REAL,
+                survey_id INTEGER NOT NULL,
+                FOREIGN KEY (survey_id) REFERENCES survey (id) ON DELETE CASCADE)
+TABLE: camera
+CREATE TABLE camera (
+                id INTEGER PRIMARY KEY,
+                name TEXT NOT NULL,
+                station_id INTEGER NOT NULL,
+                FOREIGN KEY (station_id) REFERENCES station (id) ON DELETE CASCADE)
+TABLE: uploads
+CREATE TABLE uploads (
+                id INTEGER PRIMARY KEY,
+                base_dir TEXT UNIQUE NOT NULL,
+                created_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP)
+INDEX: sqlite_autoindex_uploads_1
+None
+TABLE: media
+CREATE TABLE media (
+                id INTEGER PRIMARY KEY,
+                base_dir_id INTEGER NOT NULL,
+                relative_path TEXT UNIQUE NOT NULL,
+                sha256 TEXT UNIQUE NOT NULL,
+                ext TEXT NOT NULL,
+                timestamp TEXT NOT NULL,
+                station_id INTEGER NOT NULL,
+                camera_id INTEGER,
+                sequence_id INTEGER,
+                external_id INTEGER,
+                comment TEXT,
+                FOREIGN KEY (base_dir_id) REFERENCES uploads (id) ON DELETE CASCADE,
+                FOREIGN KEY (station_id) REFERENCES station (id) ON DELETE CASCADE,
+                FOREIGN KEY (camera_id) REFERENCES camera (id) ON DELETE SET NULL,
+                FOREIGN KEY (sequence_id) REFERENCES sequence (id) ON DELETE SET NULL)
+INDEX: sqlite_autoindex_media_1
+None
+INDEX: sqlite_autoindex_media_2
+None
+TABLE: roi
+CREATE TABLE roi (
+                id INTEGER PRIMARY KEY,
+                media_id INTEGER NOT NULL,
+                frame INTEGER NOT NULL,
+                bbox_x REAL NOT NULL,
+                bbox_y REAL NOT NULL,
+                bbox_w REAL NOT NULL,
+                bbox_h REAL NOT NULL,
+                viewpoint INTEGER,
+                reviewed INTEGER NOT NULL,
+                favorite INTEGER NOT NULL,
+                individual_id INTEGER,
+                emb INTEGER,
+                FOREIGN KEY(media_id) REFERENCES media (id) ON DELETE CASCADE,
+                FOREIGN KEY(individual_id) REFERENCES individual (id) ON DELETE SET NULL)
+TABLE: individual
+CREATE TABLE individual (
+                id INTEGER PRIMARY KEY,
+                name TEXT NOT NULL,
+                sex TEXT,
+                age TEXT)
+TABLE: sequence
+CREATE TABLE sequence (id INTEGER PRIMARY KEY)
+TABLE: media_thumbnails
+CREATE TABLE media_thumbnails (
+                id INTEGER PRIMARY KEY,
+                fid INTEGER UNIQUE NOT NULL,
+                filepath TEXT NOT NULL,
+                FOREIGN KEY(fid) REFERENCES media (id) ON DELETE CASCADE)
+INDEX: sqlite_autoindex_media_thumbnails_1
+None
+TABLE: roi_thumbnails
+CREATE TABLE roi_thumbnails (
+                id INTEGER PRIMARY KEY,
+                fid INTEGER UNIQUE NOT NULL,
+                filepath TEXT NOT NULL,
+                FOREIGN KEY(fid) REFERENCES roi (id) ON DELETE CASCADE)
+INDEX: sqlite_autoindex_roi_thumbnails_1
+None

matchypatchy-0.2.1/src/matchypatchy/config.py

@@ -0,0 +1,188 @@
+"""
+Functions for Handling Config Yaml
+
+"""
+import os
+import sys
+from pathlib import Path
+import yaml
+import animl
+
+
+class mpConfig():
+    def __init__(self, home_dir):
+        """Initiate configuration file with default values if not present"""
+
+        home_dir = Path(home_dir)
+
+        # initiate defualts
+        self.HOME_DIR = home_dir
+        self.CONFIG_PATH = home_dir / '.config.yml'
+        self.DB_DIR = home_dir / 'Database'
+        self.ML_DIR = home_dir /  'Models'
+        self.THUMBNAIL_DIR = home_dir / 'Thumbnails'
+        self.FRAME_DIR = home_dir / 'Frames'
+        self.BATCH_SIZE = 1
+        self.N_FRAMES = 3
+        self.SMART_FRAMES = True
+        self.VIDEO_FPS = 1
+        self.REID_KEY = None
+        self.VIEWPOINT_KEY = None
+        self.DETECTOR_KEY = None
+        self.KNN = 100
+        self.SEQUENCE_DURATION = 60
+        self.SEQUENCE_N = 3
+        # Check if CUDA is available and set DEVICE accordingly
+        providers = animl.get_onnx_device(quiet=True)
+        if "CUDAExecutionProvider" in providers:
+            self.DEVICE = "CUDAExecutionProvider"
+        else:
+            self.DEVICE = "CPUExecutionProvider"
+
+        # load configuration if it exists
+        if home_dir.exists():
+            self.load()
+        # create a new project folder and save
+        else:
+            home_dir.mkdir(parents=True, exist_ok=True)
+            # create necessary project folders
+            self.create_folders()
+            # save to yaml
+            self.save()
+
+    def load(self):
+        """Load configuration from the YAML file if it exists."""
+        if self.CONFIG_PATH.exists():
+            with open(self.CONFIG_PATH, 'r') as cfg_file:
+                cfg = yaml.safe_load(cfg_file)
+                self.DB_DIR = Path(cfg.get('DB_DIR', self.HOME_DIR / 'Database'))
+                self.ML_DIR = Path(cfg.get('ML_DIR', self.HOME_DIR / 'Models'))
+                self.THUMBNAIL_DIR = Path(cfg.get('THUMBNAIL_DIR', self.HOME_DIR / 'Thumbnails'))
+                self.FRAME_DIR = Path(cfg.get('FRAME_DIR', self.HOME_DIR / 'Frames'))
+                self.BATCH_SIZE = cfg.get('BATCH_SIZE', 1)
+                self.VIDEO_FPS = cfg.get('VIDEO_FPS', 1)
+                self.N_FRAMES = cfg.get('N_FRAMES', 3)
+                self.SMART_FRAMES = cfg.get('SMART_FRAMES', True)
+                
+                self.REID_KEY = cfg.get('REID_KEY', None)
+                self.VIEWPOINT_KEY = cfg.get('VIEWPOINT_KEY', None)
+                self.DETECTOR_KEY = cfg.get('DETECTOR_KEY', None)
+                self.KNN = cfg.get('KNN', 100)
+                self.SEQUENCE_DURATION = cfg.get('SEQUENCE_DURATION', 60)
+                self.SEQUENCE_N = cfg.get('SEQUENCE_N', 3)
+                self.DEVICE = cfg.get('DEVICE', "CPUExecutionProvider")
+
+        # config file not found, save the current defaults
+        else:
+            print(f"Configuration file not found at {self.CONFIG_PATH}. Saving default configuration.")
+            self.HOME_DIR.mkdir(parents=True, exist_ok=True)
+            self.set_default()
+            self.save()
+
+        # make sure all necessary directories exist
+        self.create_folders()
+
+
+    def save(self):
+        """Save the current configuration to the YAML file."""
+        output_cfg = {
+            'HOME_DIR': str(self.HOME_DIR),
+            'DB_DIR': str(self.DB_DIR),
+            'ML_DIR': str(self.ML_DIR),
+            'THUMBNAIL_DIR': str(self.THUMBNAIL_DIR),
+            'BATCH_SIZE': self.BATCH_SIZE,
+            'VIDEO_FPS': self.VIDEO_FPS,
+            'N_FRAMES': self.N_FRAMES,
+            'SMART_FRAMES': self.SMART_FRAMES,
+            'REID_KEY': self.REID_KEY,
+            'VIEWPOINT_KEY': self.VIEWPOINT_KEY,
+            'DETECTOR_KEY': self.DETECTOR_KEY,
+            'KNN': self.KNN,
+            'SEQUENCE_DURATION': self.SEQUENCE_DURATION,
+            'SEQUENCE_N': self.SEQUENCE_N,
+            'DEVICE': self.DEVICE,
+        }
+        with open(self.CONFIG_PATH, 'w') as cfg_file:
+            yaml.dump(output_cfg, cfg_file)
+
+    def set_default(self):
+        """Reset the configuration to default values."""
+        self.DB_DIR = self.HOME_DIR / 'Database'
+        self.ML_DIR = self.HOME_DIR /  'Models'
+        self.THUMBNAIL_DIR = self.HOME_DIR / 'Thumbnails'
+        self.FRAME_DIR = self.HOME_DIR / 'Frames'
+        self.BATCH_SIZE = 1
+        self.VIDEO_FPS = 1
+        self.N_FRAMES = 3
+        self.SMART_FRAMES = True
+        self.REID_KEY = None
+        self.VIEWPOINT_KEY = None
+        self.DETECTOR_KEY = None
+        self.KNN = 100
+        self.SEQUENCE_DURATION = 60
+        self.SEQUENCE_N = 3
+        if "CUDAExecutionProvider" in animl.get_onnx_device(quiet=True):
+            self.DEVICE = "CUDAExecutionProvider"
+        else:
+            self.DEVICE = "CPUExecutionProvider"
+
+    def create_folders(self):
+        """Create necessary project folders if they do not exist."""
+        self.DB_DIR.mkdir(parents=True, exist_ok=True)
+        self.ML_DIR.mkdir(parents=True, exist_ok=True)
+        self.THUMBNAIL_DIR.mkdir(parents=True, exist_ok=True)
+        self.FRAME_DIR.mkdir(parents=True, exist_ok=True)
+
+    def update(self, key_dict):
+        """Update the configuration with new key-value pairs."""
+        for key, value in key_dict.items():
+            setattr(self, key, value)
+
+        # rewrite config
+        self.save()
+
+    def update_home_dir(self, home_dir):
+        """Update the home directory and related paths."""
+        self.HOME_DIR = Path(home_dir)
+        self.DB_DIR = self.HOME_DIR / 'Database'
+        self.ML_DIR = self.HOME_DIR / 'Models'
+        self.THUMBNAIL_DIR = self.HOME_DIR / 'Thumbnails'
+        self.FRAME_DIR = self.HOME_DIR / 'Frames'
+        self.save()
+
+
+# ==============================================================================
+def resource_path(relative_path):
+    # TODO: test with installer
+    """ Get path to resource whether running in dev or installed bundle """
+    if getattr(sys, 'frozen', False):
+        return os.path.join(sys._MEIPASS, relative_path)
+
+    if "__file__" in globals() or "__file__" in locals():
+        current_location = Path(__file__).resolve()
+        if 'site-packages' in current_location.parts:
+            matchypatchy_dir = current_location.parents[0]  # Go up 1 level
+        else:
+            matchypatchy_dir = current_location.parents[2]  # Go up 2 levels
+        # Assumes this function is in src/matchypatchy/
+        return matchypatchy_dir / relative_path
+
+    return os.path.abspath(relative_path)
+
+
+def asset_path(relative_path):
+    """ Get path to resource whether running in dev or installed bundle """
+    if getattr(sys, 'frozen', False):
+        return os.path.join(sys._MEIPASS, relative_path)
+
+    if "__file__" in globals() or "__file__" in locals():
+        current_location = Path(__file__).resolve()
+
+        if 'site-packages' in current_location.parts:
+            matchypatchy_dir = current_location.parents[0]  # tbd
+        else:
+            matchypatchy_dir =current_location.parents[0]
+
+        return matchypatchy_dir / 'assets' / relative_path
+
+    return os.path.abspath(relative_path)

matchypatchy-0.2.1/src/matchypatchy/logging_config.py

@@ -0,0 +1,54 @@
+import logging
+import logging.handlers
+from pathlib import Path
+
+
+def setup_logger(log_file="matchypatchy.log", log_level=logging.INFO):
+    """
+    Setup application-wide logger that all modules can use.
+    Returns the root logger configured with file and console handlers.
+    """
+    
+    # Get root logger
+    root_logger = logging.getLogger()
+    root_logger.setLevel(log_level)
+    
+    # Remove any existing handlers to avoid duplicates
+    for handler in root_logger.handlers[:]:
+        root_logger.removeHandler(handler)
+    
+    # Create formatters
+    file_formatter = logging.Formatter(
+        '%(asctime)s - %(name)s - %(levelname)s - %(message)s',
+        datefmt='%Y-%m-%d %H:%M:%S'
+    )
+    console_formatter = logging.Formatter(
+        '%(levelname)s - %(name)s - %(message)s'
+    )
+    
+    # File handler (rotating to avoid huge log files)
+    log_path = Path(log_file)
+    file_handler = logging.handlers.RotatingFileHandler(
+        log_path,
+        maxBytes=10*1024*1024,  # 10MB
+        backupCount=5  # Keep 5 backup files
+    )
+    file_handler.setLevel(log_level)
+    file_handler.setFormatter(file_formatter)
+    root_logger.addHandler(file_handler)
+    
+    # Console handler (optional - for development)
+    console_handler = logging.StreamHandler()
+    console_handler.setLevel(logging.WARNING)  # Only warnings and errors to console
+    console_handler.setFormatter(console_formatter)
+    root_logger.addHandler(console_handler)
+    
+    return root_logger
+
+
+def get_logger(name):
+    """
+    Get a logger for a specific module.
+    Use this in all your modules: logger = get_logger(__name__)
+    """
+    return logging.getLogger(name)

matchypatchy-0.2.1/src/matchypatchy.egg-info/PKG-INFO

@@ -0,0 +1,195 @@
+Metadata-Version: 2.4
+Name: matchypatchy
+Version: 0.2.1
+Summary: GUI tool for human validation of AI-powered animal re-identification
+Author-email: Kyra Swanson <tswanson@sdzwa.org>
+Project-URL: Homepage, https://github.com/onservationtechlab/matchypatchy
+Project-URL: Issues, https://github.com/onservationtechlab/matchypatchy/issues
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: animl-lite==3.3.2
+Requires-Dist: chromadb>=1.3.4
+Requires-Dist: pyqt6>=6.9.0
+Dynamic: license-file
+
+# MatchyPatchy
+<br/>
+
+[User Manual](https://conservationtechlab.github.io/matchypatchy/)
+
+MatchyPatchy is an open-source GUI tool for human validation of AI-powered animal re-identification.\
+It was developed by the San Diego Zoo Wildlife Alliance Conservation Technology Lab.\
+Author: Kyra Swanson, (c) 2025
+<br/>
+
+---
+## Installation
+
+Matchypatchy is a stand-alone executable built in Python. Download it [here](). \
+[Github Repository](https://github.com/conservationtechlab/matchypatchy)
+<br/>
+
+---
+## Getting Started
+<br/>
+
+### Download Models
+In order to calculate potential matches, MatchyPatchy requires an animal object detector such as [MegaDetector]()
+and an embedding extractor such as [MiewID]().  Both models and more can be obtained from the SDZWA server by selecting 
+'Download Models' and checking the box associated with which models you want to download.
+<br/>
+
+### Select Survey
+In order to add media to the database, you must first specify a Survey using 
+the dropdown of available surveys. To add a new survey, 
+
+1. Select 'Manage Surveys'
+2. Select 'New' 
+3. Enter Survey Name
+4. Enter Survey Region
+5. (Optional) Enter Survey Start Year
+6. (Optional) Enter Survey End Year
+7. Select 'Ok'
+<br/>
+
+### 1. Import Images
+Images can be imported via spreadsheet or by manually selecting a directory of images.
+
+**From CSV**
+1. Select '1. Import from CSV'
+2. Open .csv file
+3. Select column headers that correspond to image Filepath, Timestamp, Survey, and Station
+4. Optionally select column headers that correspond to image Region, Sequence ID, External ID,
+    Viewpoint, Species, Individual ID, and Comment
+5. Select 'Ok'
+<br/>
+
+**From Folder**
+1. Select '1. Import from Folder'
+2. Open directory containing image files. Can be a whole Survey containg multiple Stations or single Station.
+3. Select the directory level that corresponds to Station name if available
+4. Select 'Ok'
+<br/>
+
+### 2. Process Images
+Run images through a sequence of AI models to obtain predicted matches.\
+Note: Models must be accessible in MatchyPatchy's "Models" folder - see Configuration for more.
+
+1. Select '2. Process'
+2. (Optional) Check Calculate Sequence (improves performance for videos and images captured in quick succession)
+3. **Select Detector Model** - recommended MegaDetector v5a
+4. (Optional) Select Species Classifier Model
+5. **Select Re-Indentification Model** - required to obtain predicted matches, recommended MiewIDv3
+6. (Optional) Select Viewpoint Model (improves performance by estimating animal viewpoint and limiting search space)
+<br/>
+
+### 3. Validate 
+After processing, this pageview allows you to review the imported media for errors, make changes, delete images, etc.
+It can be accessed at any time after image import. 
+<br/>
+
+Double-clicking on a cell will allow you to edit it.\
+Double-clicking on a single row will pull up a screen to edit multiple fields for an image.\
+Selecting one or more row (either by clicking on the row number or checking the select box) will enable the ability
+to mass edit particular fields, duplicate entries, or delete entries.
+<br/>
+
+The **"Show"** Option allows you view the full images or detected ROIS.\
+The **"Save"** Option saves all edits to the database.\
+The **"Undo"** Option undoes the last edit made.
+<br/>
+
+**Filters** \
+Images can be filtered by Region, Survey, Station, Species, and Individual.\
+You can also choose to show only "Unidentified" ROIs.\
+You can also display all images marked as "Favorite"
+<br/>
+
+### 4. Match
+After processing, potential matches can be validated at this pageview.
+The left side contains a **Query** image and the right side contains potential **Matches**.
+If "Calculate Sequence" was selected during the processing stage, the entire **Sequence** will be viewable on the Query side.
+The pageview will display the images and associated metadata. 
+<br/>
+
+_View Options_\
+Adjustments can be made to the **Maximum Number of Matches** shown for each image (within a sequence) and to the maximum distance
+threshold between the two images to qualify as a match. The **Cosine** or **L2** distance of the Match from the Query is displayed above the 
+match image. Select which distance metric to use in the dropdown. You must select **"Recalculate Matches"** if changes are made to either option
+in order to display those changes.\
+After matches are validated, you can **"Query by Individual"** to do quality control and ensure all images associated with
+an individual are indeed valid.\
+Images can be **Filtered** by Region, Survey, or Station to narrow the available matches shown.\
+If **"Viewpoint"** was calculated at the processing step, you can filter both the **Query** and the **Match** images by Viewpoint.\
+The **"View Data"** Button at the bottom brings you to the Media Validation pageview. 
+<br/>
+
+_Image Options_\
+You can adjust the **Brightness, Contrast** and **Sharpness** of each image, as well as **Zoom** using the mouse scroll wheel.\
+The **"Reset"** button returns the image to its original form.\
+The **"Edit Image"** option allows you to make changes to the metadata.\
+The **"Open Image"** option opens the image in your default image viewer.\
+The **"♥"** option marks the image with the "Favorite" tag.
+<br/>
+
+To confirm a match between the Query and the Match image, select the **"Match" button** in the middle, or press the 'M' or 'Space Key'.
+Pressing Match again will undo the match, asking you to confirm first.\
+You can navigate between Query Sequences and Matches by using the **"<<"** and **">>"** buttons, or by using the arrow keys.\
+You can also toggle the **Viewpoint** by pressing 'V'.
+<br/>
+
+### 5. Export
+The database can be exported as a .csv file. Simply select '5. Export' and specify the file name and location. 
+<br/>
+
+---
+## Database Management
+<br/>
+
+### Definitions
+* Survey - An ecological study employing camera traps to investigate wildlife of a particular area.
+* Region - A geographical region that may host one or more camera trap surveys.
+* Station - Reference to a physical location containing one or camera traps.
+* Species - The taxonomic and common names refering to a class of animal.
+* Media - Image (and soon video) files obtained from camera traps.
+* ROI - Regions of Interest within media files that contain animals. 
+* Individual - A particular, singular example of a given species, can be named/ID'd.
+* Sequence ID - A unique number associated with a set of sequential images or frames in a video.
+* External ID - A unique number used to reference MatchyPatchy output with other datamanagement tools.
+* Viewpoint - The side of the body of the animl facing the camera, eg "Left", "Right", "Top"
+* Comment - Notes or concerns about a particular media file
+* Favorite - A tag marking an image as noteworthy.
+<br/>
+
+### Manage Tables
+**Survey, Station,** and **Species** tables can be managed independently. 
+<br/>
+
+### CSV Import
+<br/>
+
+
+---
+## Configuration
+<br/>
+
+### Available Models
+Models currently available and compatible with MatchyPatchy:\
+_Detector Models_:
+- MegaDetector v5a
+- MegaDetector v5b
+
+_Re-ID Models_: 
+- MiewID v3
+- MiewID v2
+
+_Viewpoint Models_:
+- SDZWA Viewpoint
+<br/>
+
+### Link to New Database
+Database files can be shared across multiple users of MatchyPatchy. To link to a new .db file, 
+<br/>
+
+### Clear Data 

matchypatchy-0.2.1/src/matchypatchy.egg-info/SOURCES.txt

@@ -0,0 +1,19 @@
+LICENSE
+README.md
+pyproject.toml
+src/matchypatchy/__init__.py
+src/matchypatchy/__main__.py
+src/matchypatchy/config.py
+src/matchypatchy/logging_config.py
+src/matchypatchy.egg-info/PKG-INFO
+src/matchypatchy.egg-info/SOURCES.txt
+src/matchypatchy.egg-info/dependency_links.txt
+src/matchypatchy.egg-info/requires.txt
+src/matchypatchy.egg-info/top_level.txt
+src/matchypatchy/assets/models.yml
+src/matchypatchy/assets/schema.txt
+src/matchypatchy/assets/graphics/desktop_icon.ico
+src/matchypatchy/assets/graphics/desktop_icon.png
+src/matchypatchy/assets/graphics/fluent_pencil_icon.png
+src/matchypatchy/assets/graphics/logo.png
+src/matchypatchy/assets/graphics/thumbnail_notfound.png

matchypatchy-0.2.1/src/matchypatchy.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

matchypatchy-0.2.1/src/matchypatchy.egg-info/requires.txt

@@ -0,0 +1,3 @@
+animl-lite==3.3.2
+chromadb>=1.3.4
+pyqt6>=6.9.0

matchypatchy-0.2.1/src/matchypatchy.egg-info/top_level.txt

@@ -0,0 +1 @@
+matchypatchy