endoreg-db 0.6.0__tar.gz → 0.6.2__tar.gz

endoreg_db-0.6.2/.envrc

@@ -0,0 +1,3 @@
+source_url "https://raw.githubusercontent.com/cachix/devenv/82c0147677e510b247d8b9165c54f73d32dfd899/direnvrc" "sha256-7u4iDd1nZpxL4tCzmPG0dQgC5V+/44Ba+tHkPob1v2k="
+
+use devenv

endoreg_db-0.6.2/.gitignore

@@ -0,0 +1,179 @@
+result
+result/
+*result
+.ruff_cache/
+.devenv
+untracked_notes.md
+tests/sensitive/
+erc_data/
+./data/
+test_reports/*
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+_build
+.direnv
+
+.devenv.flake.nix
+
+###### Do not Remove ###### # Deprecated?
+# Protects temporary files from being comitted
+endoreg_client_manager/data/* 
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

endoreg_db-0.6.2/.pylintrc

@@ -0,0 +1,14 @@
+[MESSAGES CONTROL]
+disable=
+    E1101,
+    W0611,
+    C0114, ; Missing module docstring
+    C0115, ; Missing class docstring
+    C0116, ; Missing function or method docstring
+    C0301, ; Line too long
+    C0411,
+    C0412,
+    C0413, 
+    C0415, ; Import outside toplevel
+    W0613, ; Unused argument
+    W0719, ; Broad exception raised

endoreg_db-0.6.2/.python-version

@@ -0,0 +1 @@
+3.13

{endoreg_db-0.6.0 → endoreg_db-0.6.2}/PKG-INFO

@@ -1,10 +1,19 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: endoreg-db
-Version: 0.6.0
+Version: 0.6.2
 Summary: EndoReg Db Django App
-Requires-Python: >=3.11
-Description-Content-Type: text/markdown
+Project-URL: Homepage, https://info.coloreg.de
+Project-URL: Repository, https://github.com/wg-lux/endoreg-db
+Author: Max Hild, Hamza Zahid, Peter Kowalczyk
+Author-email: "Thomas J. Lux" <lux_t1@ukw.de>
+Maintainer: Max Hild, Hamza Zahid, Peter Kowalczyk
+Maintainer-email: "Thomas J. Lux" <lux_t1@ukw.de>
 License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.11
 Requires-Dist: agl-report-reader>=0.4.0
 Requires-Dist: django-bootstrap5>=24.3
 Requires-Dist: django-cors-headers>=4.7.0
@@ -27,6 +36,7 @@ Requires-Dist: scipy>=1.14.1
 Requires-Dist: tesseract>=0.1.3
 Requires-Dist: tqdm>=4.67.0
 Requires-Dist: urllib3>=2.2.3
+Description-Content-Type: text/markdown
 
 # EndoregDB - Professional Data Infrastructure for Clinical Research
 

endoreg_db-0.6.2/dev/cg.py

@@ -0,0 +1,9 @@
+from endoreg_db.case_generator.utils import get_case_generator
+from endoreg_db.case_generator.lab_sample_factory import LabSampleFactory
+
+
+TEMPLATE_NAME = "pre_default_screening_colonoscopy"
+
+cg = get_case_generator(TEMPLATE_NAME)
+lab_factory = LabSampleFactory()
+

endoreg_db-0.6.2/dev/explore_legacy_frames.py

@@ -0,0 +1,108 @@
+from tqdm import tqdm
+import os
+import json
+import shutil
+import random
+from collections import defaultdict
+
+# Define the directory paths
+base_dir = "/run/media/setup-user/8f1cd448-7aef-4eb8-9acb-d05869ea1923"
+jsons_dir = os.path.join(base_dir, "jsons")
+output_json_dir = "./jsons"
+output_image_dir = "./images"
+
+# Remove existing output directories
+shutil.rmtree(output_json_dir, ignore_errors=True)
+shutil.rmtree(output_image_dir, ignore_errors=True)
+
+# Ensure the output directories exist
+os.makedirs(output_json_dir, exist_ok=True)
+os.makedirs(output_image_dir, exist_ok=True)
+
+# Initialize dictionaries to track examples and counts
+key_stats = defaultdict(lambda: defaultdict(int))
+examples = defaultdict(list)
+
+def normalize_value(value):
+    """
+    Converts complex data types into a hashable string representation.
+    """
+    if isinstance(value, (list, dict)):
+        return str(value)
+    return value
+
+def explore_json_file(json_file):
+    """
+    Reads a JSON file and updates key_stats and examples for specific keys.
+    Also copies the corresponding image if the "path" key exists.
+    """
+    try:
+        with open(json_file, 'r', encoding='utf-8') as file:
+            data = json.loads(file.read())
+    except json.JSONDecodeError as e:
+        print(f"Error reading {json_file}: {e}")
+        return False  # Skip processing this file
+    
+    # Update key_stats and gather examples
+    extracted_keys = False
+    for key, value in data.items():
+        if key in ["predictions_smooth", "labels_new"]:
+            for sub_key, sub_value in value.items():
+                sub_value_normalized = normalize_value(sub_value)
+                key_stats[f"{key}.{sub_key}"][sub_value_normalized] += 1
+
+                # Add example if fewer than 50 have been collected
+                if len(examples[f"{key}.{sub_key}"]) < 50:
+                    examples[f"{key}.{sub_key}"].append(data)
+                    extracted_keys = True
+        else:
+            value_normalized = normalize_value(value)
+            key_stats[key][value_normalized] += 1
+    
+    # Copy the corresponding image if "path" key exists
+    if "path" in data:
+        image_path = os.path.join(base_dir, data["path"])
+        if os.path.exists(image_path):
+            try:
+                shutil.copy(image_path, output_image_dir)
+            except Exception as e:
+                print(f"Error copying image {image_path}: {e}")
+    
+    return extracted_keys
+
+def explore_directory(jsons_dir):
+    """
+    Iterates through the JSON files in a randomized order and processes them.
+    """
+    # Gather all JSON files
+    json_files = []
+    for root, _, files in os.walk(jsons_dir):
+        for file in tqdm(files):
+            if file.endswith(".json"):
+                json_files.append(os.path.join(root, file))
+    
+    # Randomize the order of JSON files
+    random.shuffle(json_files)
+
+    # Process each JSON file
+    for json_file in tqdm(json_files):
+        extracted = explore_json_file(json_file)
+
+        # Copy file if it contained relevant keys
+        if extracted:
+            shutil.copy(json_file, output_json_dir)
+
+# Start the exploration process
+explore_directory(jsons_dir)
+
+# Save key_stats and examples to separate summary files
+with open(os.path.join(output_json_dir, "key_stats.json"), "w", encoding="utf-8") as stats_file:
+    json.dump({k: dict(v) for k, v in key_stats.items()}, stats_file, indent=4)
+
+with open(os.path.join(output_json_dir, "examples.json"), "w", encoding="utf-8") as examples_file:
+    json.dump({k: [e["_id"] for e in v] for k, v in examples.items()}, examples_file, indent=4)
+
+# Display summary
+print("Exploration complete!")
+print(f"Total keys analyzed: {len(key_stats)}")
+print(f"Total examples collected: {sum(len(v) for v in examples.values())}")

endoreg_db-0.6.2/dev/test_model.py

@@ -0,0 +1,3 @@
+# run in django shell
+
+

endoreg_db-0.6.2/dev/video_utils.py

@@ -0,0 +1,46 @@
+import subprocess
+import os
+
+# /home/setup-user/dev/endoreg-db/tests/sensitive/raw_videos/001.mp4
+# /home/setup-user/dev/endoreg-db/tests/sensitive/raw_videos/001_short.mp4
+
+def copy_first_minute(input_file, output_file):
+    """
+    Copies the first minute (60 seconds) of a given MP4 file to a new file.
+    
+    Parameters:
+        input_file (str): Path to the input MP4 file.
+        output_file (str): Path to the output MP4 file.
+    """
+    # Check if the input file exists
+    if not os.path.isfile(input_file):
+        raise FileNotFoundError(f"Input file '{input_file}' does not exist.")
+    
+    # Construct the ffmpeg command
+    command = [
+        "ffmpeg",
+        "-i", input_file,          # Input file
+        "-t", "60",                # Duration to copy (60 seconds)
+        "-c", "copy",              # Copy codec (no re-encoding)
+        output_file                # Output file
+    ]
+
+    try:
+        # Run the command
+        subprocess.run(command, check=True)
+        print(f"The first minute of '{input_file}' has been saved to '{output_file}'.")
+    except subprocess.CalledProcessError as e:
+        print(f"Error during file processing: {e}")
+    except Exception as e:
+        print(f"An unexpected error occurred: {e}")
+
+# Example usage
+if __name__ == "__main__":
+    # Input and output file paths
+    input_path = "input.mp4"
+    output_path = "output_first_minute.mp4"
+
+    try:
+        copy_first_minute(input_path, output_path)
+    except Exception as error:
+        print(f"Failed: {error}")

endoreg_db-0.6.2/devenv.lock

@@ -0,0 +1,183 @@
+{
+  "nodes": {
+    "devenv": {
+      "locked": {
+        "dir": "src/modules",
+        "lastModified": 1734605856,
+        "owner": "cachix",
+        "repo": "devenv",
+        "rev": "f81cf7dc4cbfa46de11618af94e5983c5e600d8c",
+        "type": "github"
+      },
+      "original": {
+        "dir": "src/modules",
+        "owner": "cachix",
+        "repo": "devenv",
+        "type": "github"
+      }
+    },
+    "flake-compat": {
+      "flake": false,
+      "locked": {
+        "lastModified": 1733328505,
+        "owner": "edolstra",
+        "repo": "flake-compat",
+        "rev": "ff81ac966bb2cae68946d5ed5fc4994f96d0ffec",
+        "type": "github"
+      },
+      "original": {
+        "owner": "edolstra",
+        "repo": "flake-compat",
+        "type": "github"
+      }
+    },
+    "flake-utils": {
+      "inputs": {
+        "systems": "systems"
+      },
+      "locked": {
+        "lastModified": 1731533236,
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "11707dc2f618dd54ca8739b309ec4fc024de578b",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
+    "gitignore": {
+      "inputs": {
+        "nixpkgs": [
+          "pre-commit-hooks",
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1709087332,
+        "owner": "hercules-ci",
+        "repo": "gitignore.nix",
+        "rev": "637db329424fd7e46cf4185293b9cc8c88c95394",
+        "type": "github"
+      },
+      "original": {
+        "owner": "hercules-ci",
+        "repo": "gitignore.nix",
+        "type": "github"
+      }
+    },
+    "mk-shell-bin": {
+      "locked": {
+        "lastModified": 1677004959,
+        "owner": "rrbutani",
+        "repo": "nix-mk-shell-bin",
+        "rev": "ff5d8bd4d68a347be5042e2f16caee391cd75887",
+        "type": "github"
+      },
+      "original": {
+        "owner": "rrbutani",
+        "repo": "nix-mk-shell-bin",
+        "type": "github"
+      }
+    },
+    "nix2container": {
+      "inputs": {
+        "flake-utils": "flake-utils",
+        "nixpkgs": [
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1730479402,
+        "owner": "nlewo",
+        "repo": "nix2container",
+        "rev": "5fb215a1564baa74ce04ad7f903d94ad6617e17a",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nlewo",
+        "repo": "nix2container",
+        "type": "github"
+      }
+    },
+    "nixpkgs": {
+      "locked": {
+        "lastModified": 1734435836,
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "4989a246d7a390a859852baddb1013f825435cee",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "nixpkgs-unstable",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "nixpkgs-stable": {
+      "locked": {
+        "lastModified": 1734529975,
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "72d11d40b9878a67c38f003c240c2d2e1811e72a",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "nixos-24.05",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "pre-commit-hooks": {
+      "inputs": {
+        "flake-compat": "flake-compat",
+        "gitignore": "gitignore",
+        "nixpkgs": [
+          "nixpkgs"
+        ],
+        "nixpkgs-stable": "nixpkgs-stable"
+      },
+      "locked": {
+        "lastModified": 1734425854,
+        "owner": "cachix",
+        "repo": "pre-commit-hooks.nix",
+        "rev": "0ddd26d0925f618c3a5d85a4fa5eb1e23a09491d",
+        "type": "github"
+      },
+      "original": {
+        "owner": "cachix",
+        "repo": "pre-commit-hooks.nix",
+        "type": "github"
+      }
+    },
+    "root": {
+      "inputs": {
+        "devenv": "devenv",
+        "mk-shell-bin": "mk-shell-bin",
+        "nix2container": "nix2container",
+        "nixpkgs": "nixpkgs",
+        "pre-commit-hooks": "pre-commit-hooks"
+      }
+    },
+    "systems": {
+      "locked": {
+        "lastModified": 1681028828,
+        "owner": "nix-systems",
+        "repo": "default",
+        "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-systems",
+        "repo": "default",
+        "type": "github"
+      }
+    }
+  },
+  "root": "root",
+  "version": 7
+}

endoreg_db-0.6.2/devenv.nix

@@ -0,0 +1,61 @@
+{ pkgs, lib, config, inputs, ... }:
+let
+  buildInputs = with pkgs; [
+    stdenv.cc.cc
+    tesseract
+    glib
+    openssh
+  ];
+
+in 
+{
+
+  # A dotenv file was found, while dotenv integration is currently not enabled.
+  dotenv.enable = false;
+  dotenv.disableHint = true;
+
+  packages = with pkgs; [
+    cudaPackages.cuda_nvcc
+    stdenv.cc.cc
+    tesseract
+  ];
+
+  env = {
+    LD_LIBRARY_PATH = "${
+      with pkgs;
+      lib.makeLibraryPath buildInputs
+    }:/run/opengl-driver/lib:/run/opengl-driver-32/lib";
+  };
+
+  languages.python = {
+    enable = true;
+    uv = {
+      enable = true;
+      sync.enable = true;
+    };
+  };
+
+  scripts = {
+    hello.package = pkgs.zsh;
+    hello.exec = "${pkgs.uv}/bin/uv run python hello.py";
+    runtests.package = pkgs.zsh;
+    runtests.exec = "${pkgs.uv}/bin/uv run python runtests.py";
+  };
+
+  tasks = {
+  
+  };
+
+  processes = {
+  };
+
+  enterShell = ''
+    . .devenv/state/venv/bin/activate
+    runtests
+    hello
+  '';
+
+  enterTest = ''
+    nvcc -V
+  '';
+}

endoreg_db-0.6.2/devenv.yaml

@@ -0,0 +1,11 @@
+inputs:
+  nixpkgs:
+    url: github:NixOS/nixpkgs/nixpkgs-unstable
+  nix2container:
+    url: github:nlewo/nix2container
+    inputs:
+      nixpkgs:
+        follows: nixpkgs
+  mk-shell-bin:
+    url: github:rrbutani/nix-mk-shell-bin
+allowUnfree: true