diff --git a/README.md b/README.md index 7555014..8520c49 100644 --- a/README.md +++ b/README.md @@ -1,31 +1,28 @@ # Sectra Digital Pathology (DPAT) ImageAnalysis (IA) API - Software Development Kit (SDK) ## About -This is a work in progress repository providing examples on how to integrate with the Sectra IA-API. +This repository provides examples on integrating with the Sectra IA-API using python code. -Currently only a basic application exist that returns (random) results given user input. +The `examples` folder provides two examples that are suitable to get started. +Coding style is intentionally minimalistic, aiming for quick and easy reading, as we expect downstream users to apply their own style and preferences. -See the `examples` folder for more info. A roadmap is available under [milestones](https://github.com/sectra-medical/dpat_imageanalysisapi_sdk/milestones) +## Contributing -## Plan for Sectra-led contributions +We are open to accept contributions. This could be: -### 2024, January +- typed clients (e.g. implementing the API specification as dataclasses) +- further examples (likely to be placed below a `contrib/` folder) -- Invite collaborators to vet/discuss the basic example +## Planned extensions -### 2024, June +We plan on adding example code for integrating with IDS7 worklists by sending HL7v2 messages. -- Finalize image notification python examples (M1 milestone) - -### 2024, August - -- Make project fully public (remove invite-only) - -### 2024, December +## Changelog -- Finalize extended "best practices" example (M2 milestone) +### 2024-11-20 -## Changelog +- Add background image processing example ( `examples/python/ia_wholeslide` ) +- Make the repository public ### 2024-06-13 diff --git a/examples/python/README.md b/examples/python/README.md new file mode 100644 index 0000000..eaa8c4a --- /dev/null +++ b/examples/python/README.md @@ -0,0 +1,55 @@ +# Sectra Digital Pathology ImageAnalysis (IA) API + +## Getting started in python + +This document outlines how we suggest you try the examples to get started using python. + +### Prerequisites + +- We assume you have a copy of the document *"Interface Specification: Pathology Image Analysis Application Interface, Sectra Digital Pathology Module"*. At the time of writing, the most recent version was *"Verion 4.1, August 2024"*. + - This document describes all the REST endpoints and corresponding json schemas. + - Contact Sectra support for a copy, see https://my.sectra.com/en-US/support-contact/ + +- You will need to have access to a Sectra PACS with the Digital Pathology module + - We suggest you start testing in your testing Sectra PACS instance, if such an installatino is available to you. + - You will need the appropriate permissions to add and configure IA Applications in that Sectra PACS, or be in contact with someone who has + - For third party AI vendors, there is an online Sectra PACS available for a fee. Contact Sectra Support and request "discussing access to a test PACS for digital pathology AI vendors". + +- You will need ensure TCP/IP connectivity between the Sectra PACS server and the machine running your IA-APP. + - Both parties will initiate communications, so both servers need to be accessible to each other under appropiate DNS names. + +- The python examples uses the `uv` package manager, see https://docs.astral.sh/uv/getting-started/installation/ for installation. + +## 1. Starting the most basic app + +See the README in `./ia_app_basic` for more detailed instructions, TLDR: + +``` +cd examples/python/ia_app_basic +./flask_run.sh +``` + +This starts a webserver listening on 0.0.0.0:5005 (all ips, port 5005) on the machine you started it on. + +Next, you will need to register this with the Sectra PACS DPAT Server. For more detailed instructions, refer to Chapter 7 in the *System Administrator Manual*. + +- Go to https:///sectrapathologyimport/config + - log in, click Image Analysis Applications + - Under Server Side Applications, click 'register new' + - Enter the URL where your started web server (this repository) is running, as reachable from the pathology server. + - Example: `http://my-ia-app-server:5001/iademo` + - NOTE! Ensuring connectivity can take some work in most hospital environments. + - Press 'Retrieve registration Info' + - The fields should be populated, press *Save* + - Per default, the app is disabled. Click the 'disabled' button to toggle it to enabled. + +If succesful, you should now be able to right-click in any Pathology Image and select your new IA-APP (you might need to refresh any running sessions). + +TODO: screenshot here of succesful operation +TODO: screenshot of configuration UI + +## 2. A more realistic example + +TODO: Writeme + + diff --git a/examples/python/ia_app_basic/README.md b/examples/python/ia_app_basic/README.md index a2ada25..07c6edc 100644 --- a/examples/python/ia_app_basic/README.md +++ b/examples/python/ia_app_basic/README.md @@ -1,29 +1,42 @@ -pcaddemo -======== +# Sectra DPAT IA-API Example: Basic App ## About -This is a demo repository for a simple Sectra Image Analysis API (IA-API) implementation. +A very simple Sectra Image Analysis API (IA-API) implementation for a Server Side App. -Author: Martin Lindvall, martin.lindvall@sectra.com +The example is extremely barebone, with the goal to get you started and see that you manage to get the Sectra DPAT - App network connections functioning. -## Application function +For a more realistic implementation where WSI processing is done in longer-running background jobs, see `../ia_wholeslide` + +### Demo Application function - Input: User draws a polygon around a region of interest ( taggedPolygon, see `webserver.py:app_return_registerinfo` ) + - Output: a graphical primitive, or a "patch gallery" (see `webserver.py:DEMO_TYPE` and `webserver.py:app_on_userinput` ) -## Development notes +### Development notes Uses a simple flask server for responding to IA-API requests and a requests-based client for outgoing communications with the IA-API.. -For simplicity, uses no async libraries. For load-scaling, simply run with number of workers processes corresponding to expected max number of simultaneous users. Tools such as gunicorn or a similar pre-forking worker server is recommended to spawn the workers. +For simplicity, uses no async libraries. + +For load-scaling, simply run with number of workers processes corresponding to expected max number of simultaneous users. Tools such as gunicorn or a similar pre-forking worker server is recommended to spawn the workers. Should have no trouble scaling as long as number of max simultaneous users are below 1000 or so. -### Prerequisites +## Usage + +In order to try this out you'll need to + +1. Get the server within this folder running (see Install and Run) +2. Configure Sectra DPAT adding the URL of the server to the list of configured IA-Apps (see Configuring the Sectra DPAT Server) + +### Install and run + +#### Prerequisites You currently need libgeos to build shapely. On ubuntu `sudo apt install libgeos-dev`. The shapely dependency will eventually be removed. -### Install and run +#### Starting You can run this example in a virtualenv using poetry, or directly in the current python environment. @@ -40,7 +53,7 @@ pip install -e . python pcaddemo/__main__.py ``` -## Sectra Server configuration +### Configuring the Sectra DPAT Server Running this demo starts a web server on 0.0.0.0 (all local ips) listening on port 5001. @@ -62,3 +75,4 @@ If succesful, you should now be able to right-click in any Pathology Image and s ## Tested with - DPAT 3.4 on 2024-01-05 +- DPAT 4.1 on 2024-11-21 diff --git a/examples/python/ia_app_basic/pcaddemo/webserver.py b/examples/python/ia_app_basic/pcaddemo/webserver.py index e964bfa..50838c8 100644 --- a/examples/python/ia_app_basic/pcaddemo/webserver.py +++ b/examples/python/ia_app_basic/pcaddemo/webserver.py @@ -18,8 +18,6 @@ APP_NAME = "ImageAnalysisDemo" APP_MANUFACTURER = "Sectra (demo)" BIND_PORT = 5005 -DEMO_TYPE = "gallery" # use 'polygon' or 'gallery' - def json_resp(data): """serialize data to JSON and add appropriate IA-api headers""" @@ -71,7 +69,7 @@ def app_return_registerinfo(): "url": f"http://{hostname}/iademo", "manufacturer": APP_MANUFACTURER, "inputTemplate": {"type": "taggedPolygon", "content": {"tags": []}}, - "context": {}, + "context": {"gallery": False}, } return json_resp(data) @@ -90,16 +88,17 @@ def app_on_userinput(): response = {} data = request.get_json() - # save_filename = f"./debug/{data['action']}_tmp.json" - # with open(save_filename, 'w') as file: - # json.dump(data, file) + save_filename = f"./debug/userinput_{data['action']}_tmp.json" + with open(save_filename, 'w') as file: + json.dump(data, file) # data['action'] :: create, modify, delete, cancel if data["action"] == "create": - if DEMO_TYPE == "polygon": - return app_create_primitiveArea(data) - else: + use_patch_gallery = "gallery" in data["context"] and data["context"]["gallery"] + if use_patch_gallery: return app_create_patchCollection(data) + else: + return app_create_primitiveArea(data) elif data["action"] == "modify": for button in data["input"]["data"]["result"]["content"]["actions"]: if button["state"] == 1: @@ -121,12 +120,16 @@ def app_create_primitiveArea(data): this demo implementation simply returns the input geometry with a label attached """ - input_polygon = data["input"]["content"]["polygon"] - plg = sectra_polygon_to_shapely(input_polygon) - # determine suitable placement of label text - min_y_pt = reduce( - lambda pt1, pt2: pt2 if pt2[1] < pt1[1] else pt1, plg.exterior.coords - ) + # this demo app supports being configured as either type: multiArea or type: taggedPolygon + input_polygons = [] + if data["input"]["type"] == "taggedPolygon": + input_polygons = [data["input"]["content"]["polygon"]] + elif data["input"]["type"] == "multiArea": + input_polygons = data["input"]["content"]["polygons"] + + # determine suitable label placement (choose uppermost point in polygon) + all_points = [pt for polyg in input_polygons for pt in polyg["points"]] + min_y_pt = reduce(lambda pt1, pt2: pt2 if pt2["y"] < pt1["y"] else pt1, all_points) text = "0 demo-positive cells found." @@ -134,9 +137,9 @@ def app_create_primitiveArea(data): "type": "primitive", "content": { "style": {"fillStyle": None, "size": None, "strokeStyle": "#FFA500"}, - "polygons": [input_polygon], # same area as user input, + "polygons": input_polygons, # same area as user input, "labels": [ - {"location": {"x": min_y_pt[0], "y": min_y_pt[1]}, "label": text} + {"location": min_y_pt, "label": text} ], }, } @@ -233,6 +236,7 @@ def app_modify_button(button_id, data): def app_delete(data): """result has been deleted by the user, and our app is informed""" # do not intervene (will get the result deleted) + # TODO: server does not like empty response any more? return json_resp({}) diff --git a/examples/python/ia_wholeslide/.gitignore b/examples/python/ia_wholeslide/.gitignore new file mode 100644 index 0000000..37ed9b5 --- /dev/null +++ b/examples/python/ia_wholeslide/.gitignore @@ -0,0 +1,35 @@ +# Temporary Python files +*.pyc +*.egg-info +__pycache__ +.ipynb_checkpoints + +# Temporary OS files +Icon* + +# Temporary virtual environment files +/.cache/ +/.venv/ + +# Temporary server files +.env +*.pid + +# Build and release directories +/build/ +/dist/ +/debug/ +*.spec + +# Sublime Text +*.sublime-workspace + +# Eclipse +.settings + +# Don't include +scripts +.python-version + +data/queue +data/requests diff --git a/examples/python/ia_wholeslide/README.md b/examples/python/ia_wholeslide/README.md new file mode 100644 index 0000000..34d99f6 --- /dev/null +++ b/examples/python/ia_wholeslide/README.md @@ -0,0 +1,141 @@ +# Sectra DPAT IA-API Example: Background Processing + +## About +Example of a fairly robust Sectra Image Analysis API (IA-API) implementation for a Server Side App. + +The example consists of a `webserver.py` and workers started through `worker.py` + +### Demo Application function +The *webserver* implements the DPAT IA-API and will respond to user manually triggering analysis as well as automatic image notifications sent on image import. + +Upon receiving a request, the webserver will immediately send an "in progress" result back which is visualized on the slide to the user (in the manual scenario) or to any user that opens the image (so it works for image notification requests as well). + +The webserver writes a request to disk-based queue. If at least one `worker.py` is running, it will process these requests by + +- Storing slide and case metadata +- Downloading and storing a thumbnail of the WSI and the slide label image +- Downloading the WSI file(s) +- Running a dummy processing job (time.sleep) +- Changing the in-progress result to the real proper result + +During the above operations, the in-progress result is updated to reflect processing status to any user viewing the slide. + +In order to process more requests at once, start more `worker.py` processes. To run them on multiple servers, ensure the queue directory is on a *samba* cifs fileshare (samba supports flock() needed for the queue locking). + +Summary: + +- Input: Image Notification push request, or user-triggered by selecting the app in the right-click context menu of a slide. +- Output: a graphical primitive (a square with a dummy computed answer) + +### Development notes +Uses a simple flask server for responding to IA-API requests and a requests-based client for outgoing communications with the IA-API.. + +For simplicity, uses no async libraries. + +For load-scaling, you need to mind incoming web request scaling and background workers. + +For scaling the webserver, simply run with number of webserver processes corresponding to expected max number of simultaneous users. Tools such as gunicorn or a similar pre-forking server is recommended to spawn the webserver workers. +Should have no trouble scaling as long as number of max simultaneous users are below 1000 or so. + +For worker scaling, run a number of workers corresponding so that compute resources on your node is maximized. If more are needed, +move the queue directory to a fileshare so that multiple machines can spawn worker processes and read it. + +## Usage + +In order to try this out you'll need to + +1. Get the server and worker within this folder running (see Install and Run) +2. Configure Sectra DPAT adding the URL of the server to the list of configured IA-Apps (see Configuring the Sectra DPAT Server) + +### Install and run + +#### Prerequisites +We use astral `uv` for python dependency management. Please install it first. See https://docs.astral.sh/uv/ for more install options. + +``` +curl -LsSf https://astral.sh/uv/install.sh | sh +``` + +Since the code uses file-based locks, **running multiple workers is only supported on Linux/POSIX-systems**. + +#### Starting +Start the webserver: + +``` +./flask_run.sh +``` + +Starting one background worker process: + +``` +./worker_run.sh +``` + +### Configuring the Sectra DPAT Server + +The webserver starts on 0.0.0.0 (all local ips) listening on port 5006. + +You need to configure the Sectra Pathology Server (SPS) to call this server. This involves: + +1. Ensuring that the SPS can reach this host over the network (ensure there is a route and that firewall rules allow it) +2. Registering the IA-API app in the configuration interface (see chapter 7 in the System Administrator Manual) + - in brief: goto https:///sectrapathologyimport/config + - log in, click Image Analysis Applications + - Under Server Side Applications, click 'register new' + - Enter the URL where your started web server (this repository) is running, as reachable from the pathology server. Example: `http://my-ia-app-server:5006/dpat_ia_app_demo/wholeslide` + - Press 'Retrieve registration Info' + - If you want to try Image Notifications, switch it to Enabled + - NOTE! The app will receive notifications for all imported WSI and currently does not reject any based on metadata. Since the app downloads the WSI, you will receive a copy of all WSI on your app server. + - The fields should be populated, press *Save* + - Per default, the app is disabled. Click the 'disabled' button to toggle it to enabled. + +If succesful, you should now be able to right-click in any Pathology Image and select your new IA-APP (you might need to refresh any running sessions). + +### Development and Testing + +You can manually (re)-process a single slide using the worker CLI. + +``` +$ python ./src/dpat_wholeslide/worker.py --help + +Usage: worker.py [OPTIONS] COMMAND [ARGS]... + +Options: + --help Show this message and exit. + +Commands: + process process single slide + watch start monitoring for WSI processing requests +``` + +Actually, the `worker_run.sh` script mentioned above just calls the `watch` subcommand of the worker cli. + +The `webserver.py` process will create "slide folders" within `./data/requests` when a user calls the app. The watch process +monitors the folder for such files and automatically processes them. However, you can also run manually using the same info, +which is useful while you are developing your analysis code. + +Example: + - Only start the webserver, do not start any workers + - Go to a slide and trigger your configured app + - Note that a folder has been created below `./data/requests`, e.g. `./data/requests/AI-DRBR-290/A-HE-9adf3d8c20` + - Now trigger processing on this folder: + - Execute `uv run -- python ./src/dpat_wholeslide/worker.py ./data/requests/AI-DRBR-290/A-HE-9adf3d8c20` + - Investigate the slide folder now and you'll note that it has the following files + - `metadata.json` -- persisted metadata about the slide being processed + - `thumbnail.jpg` -- a thumbnail of the slide + - `label.jpg` -- the slide label image (if available, not all WSI have them) + - a folder `wsi_files/` -- containing the entire WSI + +## Changes needed to use in production + +This example code is intended to get you started. Hence it avoids a few things you would need to do when using it for production + +We suggest you at least: + +- Ensure you scale webserver workers using a WSGI runner like gunicorn +- Ensure you clean up WSI files and metadata after some suitable period in your worker watch loop + +## Tested with + +- DPAT 3.4 on 2024-01-05 +- DPAT 4.1 on 2024-11-21 diff --git a/examples/python/ia_wholeslide/flask_run.bat b/examples/python/ia_wholeslide/flask_run.bat new file mode 100644 index 0000000..2e5c862 --- /dev/null +++ b/examples/python/ia_wholeslide/flask_run.bat @@ -0,0 +1,4 @@ +set FLASK_APP=src\dpat_wholeslide\webserver +set FLASK_RUN_PORT=5006 +set FLASK_DEBUG=1 +uv run -- flask run diff --git a/examples/python/ia_wholeslide/flask_run.sh b/examples/python/ia_wholeslide/flask_run.sh new file mode 100755 index 0000000..05c8a59 --- /dev/null +++ b/examples/python/ia_wholeslide/flask_run.sh @@ -0,0 +1,6 @@ +#!/bin/bash +export FLASK_APP=src/dpat_wholeslide/webserver +export FLASK_RUN_PORT=5006 +export FLASK_RUN_HOST=0.0.0.0 +export FLASK_DEBUG=1 +uv run -- flask run diff --git a/examples/python/ia_wholeslide/pyproject.toml b/examples/python/ia_wholeslide/pyproject.toml new file mode 100644 index 0000000..f0a84af --- /dev/null +++ b/examples/python/ia_wholeslide/pyproject.toml @@ -0,0 +1,25 @@ +[project] +name = "dpat-wholeslide" +version = "0.1.0" +description = "Add your description here" +authors = [ + { name = "Martin Lindvall", email = "martin.lindvall@sectra.com" } +] +requires-python = ">=3.11" +dependencies = [ + "flask>=3.0.3", + "requests-toolbelt>=1.0.0", + "requests>=2.32.3", + "tqdm>=4.67.0", + "pillow>=11.0.0", +] + +[build-system] +requires = ["hatchling"] +build-backend = "hatchling.build" + +[dependency-groups] +dev = [ + "black>=24.10.0", + "ipykernel>=6.29.5", +] diff --git a/examples/python/ia_wholeslide/src/dpat_wholeslide/__init__.py b/examples/python/ia_wholeslide/src/dpat_wholeslide/__init__.py new file mode 100644 index 0000000..fcf3363 --- /dev/null +++ b/examples/python/ia_wholeslide/src/dpat_wholeslide/__init__.py @@ -0,0 +1,3 @@ +""" dpat_wholeslide """ + +from .version import __version__ diff --git a/examples/python/ia_wholeslide/src/dpat_wholeslide/__main__.py b/examples/python/ia_wholeslide/src/dpat_wholeslide/__main__.py new file mode 100644 index 0000000..12b15b6 --- /dev/null +++ b/examples/python/ia_wholeslide/src/dpat_wholeslide/__main__.py @@ -0,0 +1,6 @@ +#!/usr/bin/env python + +if __name__ == "__main__": + from dpat_wholeslide.webserver import app, BIND_PORT + + app.run(host="0.0.0.0", port=BIND_PORT, debug=False) diff --git a/examples/python/ia_wholeslide/src/dpat_wholeslide/dzidesc.py b/examples/python/ia_wholeslide/src/dpat_wholeslide/dzidesc.py new file mode 100644 index 0000000..65ecf95 --- /dev/null +++ b/examples/python/ia_wholeslide/src/dpat_wholeslide/dzidesc.py @@ -0,0 +1,352 @@ +""" +dzidesc -- module for common computations done on DeepZoomImage images + + +DziDescription <--- represents an entire zoomable image + | + | there are fixed steps of zooms that can be retrieved, named levels + | + | + +---- DziLevel <-- the baselevel is the largest and decreasing numbers mean smaller images. + | + | + | + +--- DziTile <-- each level consists of columns * rows tiles that are each maximum + (patch_size, patch_size), but might be smaller at the edges of the image. + +Example Usage: + + d = DziDescription(87647, 76723, 240) + for level in d.levels(): + print(level) + +Outputs: + + + + + + + + + + + + + + + + + + +""" + +import collections +import math +from typing import List, Generator, Tuple + +from dpat_wholeslide.geometry import Point, Rect + + +def dzilevel_at_size(width, height) -> int: + return int(math.ceil(math.log2(max(width, height)))) + + +def dzilevel_scale_factor_inv(level, max_level) -> float: + """inverse of dzilevel_scale_factor""" + # return math.pow(0.5, max_level - level) + return 1.0 / dzilevel_scale_factor(level, max_level) + + +def dzilevel_scale_factor(level, max_level) -> float: + # return 1 << (max_level - level) + return 2.0 ** (max_level - level) + + +# DziTileToImageDescr :: describes how and where a tile should be written when extracting an area +# first crop to crop, then place the resulting img into larger data area as designated by place_point +DziTileToImageDescr = collections.namedtuple( + "DziTileToImageDescr", ["tile", "crop", "place_point"] +) + + +class DziDescription: + """ + Utility class for DeepZoomImage calculations + """ + + def __init__( + self, + base_width: int, + base_height: int, + tile_size: int, + tile_overlap: int = 0, + magnification: float | None = None, + resolution: float | None = None, + ): + self.width = base_width + self.height = base_height + self.tile_size = tile_size + self.tile_overlap = tile_overlap + self.magnification = magnification + self.resolution = resolution + self.format = "jpeg" + + def baselevel(self) -> int: + return dzilevel_at_size(self.width, self.height) + + def maxlevel(self) -> int: + return self.baselevel() + + def level(self, level: int) -> "DziLevel": + return DziLevel(self, level) + + def levels(self) -> List["DziLevel"]: + return [self.level(x) for x in range(2, self.maxlevel() + 1)] + + def level_approx_width(self, width: int): + # first level with .width() >= width + if width >= self.width: + return self.level(self.baselevel()) + return next(filter(lambda x: x.width() >= width, self.levels())) + + def level_at_mag(self, magn: float): + """get DziLevel for given magnification""" + if not self.magnification: + raise Exception( + "magnification not set on this instance, method not available." + ) + if magn > self.magnification: + raise ValueError( + "requested magnification {} is larger than slide's max {}".format( + magn, self.magnification + ) + ) + mag_diff = self.magnification / magn + level_diff = int(round(math.log2(mag_diff))) + lvl = self.baselevel() - level_diff + return self.level(lvl) + + def level_at_mpp(self, microns_per_pixel: float, always_smaller=False): + """ + get lvl closest to requested resolution + + if always_smaller is True, will always return the higher-resolution level (lower mpp) + """ + if not self.resolution: + raise Exception( + "resolution not set on this instance, method not available." + ) + slideres = self.resolution + res_diff = microns_per_pixel / slideres + level_diff = int(round(math.log2(res_diff))) + if always_smaller: + level_diff = math.floor(math.log2(res_diff)) + if res_diff < 1.0: + level_diff = 0 # no such level available + lvl = self.baselevel() - level_diff + lvl_dzi = self.level(lvl) + mpp_at_level = lvl_dzi.resolution() + return (lvl_dzi, mpp_at_level, mpp_at_level / microns_per_pixel) + + def __repr__(self): + return "".format( + self.width, self.height, self.tile_size, self.tile_overlap, self.baselevel() + ) + + +class DziLevel(object): + """represents a single Dzi Level within a DZI""" + + def __init__(self, parent: DziDescription, level: int): + self.parent = parent + self.level = level + self.n_cols = self.cols() + self.n_rows = self.rows() + + def level_scale(self) -> float: + return dzilevel_scale_factor_inv(self.level, self.parent.baselevel()) + + def level_scale_inv(self) -> float: + # yes, naming is confusing. here for backward compat. + return dzilevel_scale_factor(self.level, self.parent.baselevel()) + + def cols(self) -> int: + return int(math.ceil((self.width() * 1.0) / self.parent.tile_size)) + + def rows(self) -> int: + return int(math.ceil((self.height() * 1.0) / self.parent.tile_size)) + + def width(self): + return int(max(1, math.floor(self.parent.width * self.level_scale()))) + + def height(self): + return int(max(1, math.floor(self.parent.height * self.level_scale()))) + + def size(self) -> Tuple[int, int]: + return (self.width(), self.height()) + + def n_tiles(self) -> int: + """total number of tiles in level""" + return self.cols() * self.rows() + + def magnification(self) -> float | None: + """get the magnification of this level, i.e 20.0 for 20X etc.""" + if self.parent.magnification is None: + return None + return self.parent.magnification * self.level_scale() + + def resolution(self) -> float | None: + """get the resolution of this level in microns per pixel""" + if self.parent.resolution is None: + return None + return self.parent.resolution * self.level_scale_inv() + + def tile(self, col, row): + return DziTile(self, col, row) + + def tiles(self) -> Generator["DziTile", None, None]: + # images are usually written in stripes, so by col. is faster + return self.tiles_bycol() + + def tiles_byrow(self) -> Generator["DziTile", None, None]: + for c in range(0, self.cols()): + for r in range(0, self.rows()): + yield self.tile(c, r) + + def tiles_bycol(self) -> Generator["DziTile", None, None]: + for r in range(0, self.rows()): + for c in range(0, self.cols()): + yield self.tile(c, r) + + def tiles_within(self, x, y, width, height) -> Generator["DziTile", None, None]: + """ + list tiles that intersect with area of given bounding box + + x,y = top left position of bbox, absolute pixels + """ + col_start = math.floor(x / self.parent.tile_size) + col_end = math.floor((x + width) / self.parent.tile_size) + row_start = math.floor(y / self.parent.tile_size) + row_end = math.floor((y + height) / self.parent.tile_size) + for r in range(max(row_start, 0), min(row_end + 1, self.rows())): + for c in range(max(col_start, 0), min(col_end + 1, self.cols())): + yield self.tile(c, r) + + def tiles_for_area( + self, x, y, width, height + ) -> Generator["DziTileToImageDescr", None, None]: + """ + get a DziTileToImageDescr that describes tiles to fetch and how to crop them to get requested area + + x,y = top left position of bbox, absolute pixels + """ + tiles = self.tiles_within(x, y, width, height) + for tile in tiles: + place_origin = Point( + tile.col * self.parent.tile_size, tile.row * self.parent.tile_size + ) + place_dest = place_origin - Point(x, y) + crop = tile.crop.clone() + if place_dest.x < 0: + crop.left += abs(place_dest.x) + place_dest.x = 0 + if place_dest.y < 0: + crop.top += abs(place_dest.y) + place_dest.y = 0 + yield DziTileToImageDescr(tile, crop, place_dest) + + def tiles_for_level(self): + return self.tiles_for_area(0, 0, self.width(), self.height()) + + def __repr__(self): + return "".format( + self.level, self.cols(), self.rows(), self.size() + ) + + +class DziTile: + """a single tile within a parent DziLevel""" + + def __init__(self, level: DziLevel, col: int, row: int): + self.parent = level + self.level = level.level + self.col = col + self.row = row + if col >= self.parent.n_cols: + raise Exception(f"column {col} out of bounds for level {level}") + if row >= self.parent.n_rows: + raise Exception(f"row {row} out of bounds for level {level}") + overlap = self.parent.parent.tile_overlap + t, l, r, b = (overlap, overlap, overlap, overlap) # (l,t,r,b) + if overlap > 0: + if self.col == 0: + l = 0 + if self.col == self.parent.n_cols - 1: + r = 0 + if self.row == 0: + t = 0 + if self.row == self.parent.n_rows - 1: + b = 0 + self.overlap = (t, l, r, b) + tile_size = self.parent.parent.tile_size + self.width = tile_size + l + r + self.height = tile_size + t + b + if self.col == self.parent.n_cols - 1: + # final column + remainder = self.parent.width() % tile_size + if remainder == 0: + remainder = tile_size + self.width = remainder + l + r + if self.row == self.parent.n_rows - 1: + # final row + remainder = self.parent.height() % tile_size + if remainder == 0: + remainder = tile_size + self.height = remainder + t + b + bottom_left = Point(tile_size + l, tile_size + t).clip( + Rect((0, 0), (self.width, self.height)) + ) + self.top_left = Point( + self.col * tile_size, self.row * tile_size + ) # placement if overlap is ignored + self.crop = Rect((l, t), bottom_left) + + def __repr__(self): + return "".format( + self.level, self.col, self.row + ) + + def to_path(self): + return "{0}/{1}_{2}".format(self.level, self.col, self.row) + + +if __name__ == "__main__": + # Example Usage: + + # list levels and tiles + d = DziDescription(87647, 76723, 240) + # d.tile_overlap = 0 + print(d) + + # %% + print(" -- listing levels:") + for level in d.levels(): + print(level) + for tile in level.tiles(): + pass + # print(tile) + + # %% find suitable level + print("\nfinding approximate width=2000 level:") + l = d.level_approx_width(2000) + print(l) + + # %% get tiles in bbox + for tile in l.tiles_within(512, 418, 1212, 400): + print(tile) + + # %% get tile dest descriptor + l = d.level_approx_width(2000) + for tile in l.tiles_for_area(512, 2150, 520, 400): + print(tile) diff --git a/examples/python/ia_wholeslide/src/dpat_wholeslide/geometry.py b/examples/python/ia_wholeslide/src/dpat_wholeslide/geometry.py new file mode 100644 index 0000000..802f076 --- /dev/null +++ b/examples/python/ia_wholeslide/src/dpat_wholeslide/geometry.py @@ -0,0 +1,251 @@ +""" +Basic geometry classes + +Point -- point with (x,y) coordinates +Rect -- two points, defining a rectangle + +Modified from https://wiki.python.org/moin/PointsAndRectangles and indicated to be in the Public Domain. +""" + +import math + + +class Point: + """A point identified by (x,y) coordinates. + + supports: +, -, *, /, str, repr + + length -- calculate length of vector to point from origin + distance_to -- calculate distance between two points + as_tuple -- construct tuple (x,y) + clone -- construct a duplicate + integerize -- convert x & y to integers + floatize -- convert x & y to floats + move_to -- reset x & y + rotate -- rotate around the origin + rotate_about -- rotate around another point + """ + + def __init__(self, x=0.0, y=0.0): + self.x = x + self.y = y + + def __add__(self, p): + """Point(x1+x2, y1+y2)""" + return Point(self.x + p.x, self.y + p.y) + + def __sub__(self, p): + """Point(x1-x2, y1-y2)""" + return Point(self.x - p.x, self.y - p.y) + + def __mul__(self, scalar): + """Point(x1*x2, y1*y2)""" + return Point(self.x * scalar, self.y * scalar) + + def __truediv__(self, scalar): + """Point(x1/x2, y1/y2)""" + return Point(self.x / scalar, self.y / scalar) + + def __str__(self): + return "(%s, %s)" % (self.x, self.y) + + def __repr__(self): + return "%s(%r, %r)" % (self.__class__.__name__, self.x, self.y) + + def length(self): + return math.sqrt(self.x**2 + self.y**2) + + def distance_to(self, p): + """Calculate the distance between two points.""" + return (self - p).length() + + def as_tuple(self): + """(x, y)""" + return (self.x, self.y) + + def clone(self): + """Return a full copy of this point.""" + return Point(self.x, self.y) + + def map(self, fn): + """ + transform x,y with fn + + fn(scalar) -> scalar + """ + return Point(fn(self.x), fn(self.y)) + + def integerize(self): + """Convert co-ordinate values to integers.""" + return self.map(int) + + def floatize(self): + """Convert co-ordinate values to floats.""" + return self.map(float) + + def rotate(self, rad): + """Rotate counter-clockwise by rad radians. + + Positive y goes *up,* as in traditional mathematics. + + Interestingly, you can use this in y-down computer graphics, if + you just remember that it turns clockwise, rather than + counter-clockwise. + + The new position is returned as a new Point. + """ + s, c = [f(rad) for f in (math.sin, math.cos)] + x, y = (c * self.x - s * self.y, s * self.x + c * self.y) + return Point(x, y) + + def rotate_about(self, p, theta): + """Rotate counter-clockwise around a point, by theta degrees. + + Positive y goes *up,* as in traditional mathematics. + + The new position is returned as a new Point. + """ + return ((self - p).rotate(theta)) + p + + def clip(self, rect): + """ensure Point is max_x or max_y""" + x = max(min(self.x, rect.bottom_right.x), rect.top_left.x) + y = max(min(self.y, rect.bottom_right.y), rect.top_left.y) + return Point(x, y) + + +class Rect: + """A rectangle identified by two points. + + The rectangle stores left, top, right, and bottom values. + + Coordinates are based on screen coordinates. + + origin top + +-----> x increases | + | left -+- right + v | + y increases bottom + + set_points -- reset rectangle coordinates + contains -- is a point inside? + overlaps -- does a rectangle overlap? + top_left -- get top-left corner + bottom_right -- get bottom-right corner + expanded_by -- grow (or shrink) + """ + + def __init__(self, pt1, pt2): + """Initialize a rectangle from two points.""" + if not isinstance(pt1, Point): + pt1 = Point(pt1[0], pt1[1]) + if not isinstance(pt2, Point): + pt2 = Point(pt2[0], pt2[1]) + self.set_points(pt1, pt2) + + @classmethod + def from_bbox(cls, left, top, width, height): + """initialize from a bounding box""" + return cls((left, top), (left + width, top + height)) + + @classmethod + def from_bounds(cls, minx, miny, maxx, maxy): + """initialize from a bounds box (i.e, shapely)""" + return cls((minx, miny), (maxx, maxy)) + + @property + def top_left(self): + """Return the top-left corner as a Point.""" + return Point(self.left, self.top) + + @property + def bottom_right(self): + """Return the bottom-right corner as a Point.""" + return Point(self.right, self.bottom) + + @property + def width(self): + return self.right - self.left + + @property + def height(self): + return self.bottom - self.top + + def __add__(self, p): + return Rect(self.top_left + p, self.bottom_right + p) + + def __sub__(self, p): + return Rect(self.top_left - p, self.bottom_right - p) + + def __mul__(self, scalar): + return Rect(self.top_left * scalar, self.bottom_right * scalar) + + def __truediv__(self, scalar): + return Rect(self.top_left / scalar, self.bottom_right / scalar) + + def set_points(self, pt1, pt2): + """Reset the rectangle coordinates.""" + (x1, y1) = pt1.as_tuple() + (x2, y2) = pt2.as_tuple() + self.left = min(x1, x2) + self.top = min(y1, y2) + self.right = max(x1, x2) + self.bottom = max(y1, y2) + + def contains(self, pt): + """Return true if a point is inside the rectangle.""" + x, y = pt.as_tuple() + return self.left <= x <= self.right and self.top <= y <= self.bottom + + def overlaps(self, other): + """Return true if a rectangle overlaps this rectangle.""" + return ( + self.right > other.left + and self.left < other.right + and self.top < other.bottom + and self.bottom > other.top + ) + + def expanded_by(self, n): + """Return a rectangle with extended borders. + + Create a new rectangle that is wider and taller than the + immediate one. All sides are extended by "n" points. + """ + p1 = Point(self.left - n, self.top - n) + p2 = Point(self.right + n, self.bottom + n) + return Rect(p1, p2) + + def map(self, fn): + """transform rect by appling fn to all scalar values""" + return Rect(self.top_left.map(fn), self.bottom_right.map(fn)) + + def as_tuple(self): + return (self.left, self.top, self.right, self.bottom) + + def as_bbox(self): + return (self.left, self.top, self.width, self.height) + + def clone(self): + """Return a full copy of this Rect.""" + return Rect(self.top_left, self.bottom_right) + + def __str__(self): + return "" % (self.left, self.top, self.right, self.bottom) + + def __repr__(self): + return "%s(%r, %r)" % ( + self.__class__.__name__, + Point(self.left, self.top), + Point(self.right, self.bottom), + ) + + +# %% + +if __name__ == "__main__": + p = Point(5, 2) + print(p.as_tuple()) + + b = Rect((10, 10), (40, 40)) + print(b.as_bbox()) diff --git a/examples/python/ia_wholeslide/src/dpat_wholeslide/locks.py b/examples/python/ia_wholeslide/src/dpat_wholeslide/locks.py new file mode 100644 index 0000000..cf393cd --- /dev/null +++ b/examples/python/ia_wholeslide/src/dpat_wholeslide/locks.py @@ -0,0 +1,40 @@ +""" +module for flock-based locks (work on POSIX filesystems through the Linux kernel) +""" + +import os +import time +import fcntl + + +def lock_acquire(lock_file, timeout=5.0): + start_time = current_time = time.time() + while current_time < start_time + timeout: + lock_file_fd = lock_try_acquire(lock_file) + if lock_file_fd: + return lock_file_fd + time.sleep(0.5) + current_time = time.time() + + +def lock_try_acquire(lock_file): + open_mode = os.O_RDWR | os.O_CREAT | os.O_TRUNC + fd = os.open(lock_file, open_mode) + lock_file_fd = None + try: + fcntl.flock(fd, fcntl.LOCK_EX | fcntl.LOCK_NB) + except (IOError, OSError): + pass + else: + lock_file_fd = fd + + if lock_file_fd is None: + os.close(fd) + + return lock_file_fd + + +def lock_release(lock_file_fd): + fcntl.flock(lock_file_fd, fcntl.LOCK_UN) + os.close(lock_file_fd) + return None diff --git a/examples/python/ia_wholeslide/src/dpat_wholeslide/py.typed b/examples/python/ia_wholeslide/src/dpat_wholeslide/py.typed new file mode 100644 index 0000000..e69de29 diff --git a/examples/python/ia_wholeslide/src/dpat_wholeslide/utils.py b/examples/python/ia_wholeslide/src/dpat_wholeslide/utils.py new file mode 100644 index 0000000..c9ad827 --- /dev/null +++ b/examples/python/ia_wholeslide/src/dpat_wholeslide/utils.py @@ -0,0 +1,31 @@ +""" +Utilities +""" + +from functools import partial + +import requests + +from dpat_wholeslide.version import ( + SECTRA_IA_API_MIN_VERSION, +) + + +def requests_session_from_callbackinfo(callback_info): + bearer_token = callback_info["token"] + url = callback_info["url"].rstrip("/") + "/" + s = requests.Session() + # uncomment s.verify below if you do not yet have a valid certificate + # s.verify = False + s.headers.update( + { + "Authorization": f"Bearer {bearer_token}", + "X-Sectra-ApiVersion": f"{SECTRA_IA_API_MIN_VERSION}", + } + ) + + def new_request(prefix, f, method, url, *args, **kwargs): + return f(method, prefix + url, *args, **kwargs) + + s.request = partial(new_request, url, s.request) + return s diff --git a/examples/python/ia_wholeslide/src/dpat_wholeslide/version.py b/examples/python/ia_wholeslide/src/dpat_wholeslide/version.py new file mode 100644 index 0000000..68c7cd1 --- /dev/null +++ b/examples/python/ia_wholeslide/src/dpat_wholeslide/version.py @@ -0,0 +1,24 @@ +""" +version info +""" + +__version__ = "0.1.0" + +# this is the minimum version we require, we do not support +# servers that run earlier versions. +# +# Bump this number when you add expectations on API datastructures or endpoints only +# present from version X.Y onward. +# +# 1.5 here corresponds to DPAT 3.0 and we make use of /slides//info endpoint +# only available from this version and onward +SECTRA_IA_API_MIN_VERSION = "1.5" + +# this is the highest version we've explicitly tested with +# higher-capable servers should fallback to this api version to ensure compatability +# +# Bump this to the highest number you've tested with. +# If you are lazy, set: +# SECTRA_IA_API_MAX_VERSION = SECTRA_IA_API_MIN_VERSION +# (you might lose some enhancements that you do not rely on anyway) +SECTRA_IA_API_MAX_VERSION = "1.8" diff --git a/examples/python/ia_wholeslide/src/dpat_wholeslide/webserver.py b/examples/python/ia_wholeslide/src/dpat_wholeslide/webserver.py new file mode 100755 index 0000000..301c494 --- /dev/null +++ b/examples/python/ia_wholeslide/src/dpat_wholeslide/webserver.py @@ -0,0 +1,272 @@ +import json +import traceback +import hashlib + +from datetime import datetime +from pathlib import Path + +from flask import Flask, request, jsonify + +from dpat_wholeslide.version import ( + __version__, + SECTRA_IA_API_MIN_VERSION, +) +from dpat_wholeslide.utils import requests_session_from_callbackinfo + +app = Flask(__name__) + +APP_NAME = "demo-wholeslide" +APP_MANUFACTURER = "Sectra (demo)" +BIND_PORT = 5006 + +# -------- Utils -------- + + +def json_resp(data): + """serialize response data to JSON and add appropriate IA-api headers""" + resp = jsonify(data) + resp.headers.set("X-Sectra-ApiVersion", SECTRA_IA_API_MIN_VERSION) + resp.headers.set("X-Sectra-SoftwareVersion", __version__) + return resp + + +# ----------------------- + + +@app.route("/", methods=["GET"]) +def index(): + """ + Just a hello world page. The json is not part of the Sectra API. + Useful for debugging a running service. + """ + return json_resp( + [ + { + "name": APP_NAME, + "version": __version__, + "route": "/dpat_ia_app_demo/wholeslide", + "sectra-apiversion": SECTRA_IA_API_MIN_VERSION, + } + ] + ) + + +# IA-API Implementation +# ===================== + + +@app.route("/dpat_ia_app_demo/wholeslide/info", methods=["GET"]) +def app_return_info(): + """ + route returning application info according to the DPAT IA API specification + """ + data = {"apiVersion": SECTRA_IA_API_MIN_VERSION, "softwareVersion": __version__} + return json_resp(data) + + +@app.route("/dpat_ia_app_demo/wholeslide", methods=["GET"]) +def app_return_registerinfo(): + """ + route for user-assisted registration in the SectraPathologyImport/config UI + + This URL is what should go into the configure URL + """ + hostname = f"127.0.0.1:{BIND_PORT}" + if "Host" in request.headers: + # return whatever hostname the requesting client sent to us + # so if the user types in http://some-hostname/dpat_ia_app_demo/wholeslide + # we return that same hostname + hostname = request.headers["Host"] + + # NOTE: as of DPAT 3.4 / IA-API v1.8 this will prepopulate all fields in the registration + # **except** Image Notifications. So if you need Notifications you must tell the admin who configs the application + # to enable it (click the checkbox when registering). + data = { + "applicationId": APP_NAME, + "displayName": APP_NAME, + "url": f"http://{hostname}/dpat_ia_app_demo/wholeslide", + "manufacturer": APP_MANUFACTURER, + "inputTemplate": {"type": "wholeSlide"}, + "context": {}, + } + return json_resp(data) + + +@app.route("/dpat_ia_app_demo/wholeslide", methods=["POST"]) +def app_on_userinput(): + """ + Dispatch (routing) for user operations. + + This route is called when the app is activated by the user through the right-click context menu + """ + response = {} + data = request.get_json() + + # data['action'] :: create, modify, delete, cancel + if data["action"] == "create": + # called when user selects this app from interactive menu + return app_add_wsi_to_processing_queue(data) + elif data["action"] == "modify": + # this is never called for our app since we dont return modifiable results + pass + elif data["action"] == "delete": + # called when user deletes annotation (result) created by this app + return app_delete(data) + elif data["action"] == "cancel": + return json_resp([]) + return json_resp(response) + + +@app.route("/dpat_ia_app_demo/wholeslide/imagenotification", methods=["POST"]) +def app_on_imagenotification(): + data = request.get_json() + app_add_wsi_to_processing_queue(data) + # specification says we should return 200, empty + return json_resp({}) + + +# ========================================= + + +def app_add_wsi_to_processing_queue(data): + """ + request processing of one WSI. + + persist basic metadata about the WSI and the auth token to disk, so that workers can process it further in the background + (see worker.py) + """ + slide_id = data["slideId"] + + # fetch basic slide metadata + api = requests_session_from_callbackinfo(data["callbackInfo"]) + r = api.get(f"slides/{slide_id}/info?scope=extended&includePHI=true") + r.raise_for_status() # raise on error + metadata = r.json() + + # persist user request in a file-based queue + # in this example we use PHI data since it makes the app easier to debug/test -- because it gives + # stable human-readble identities. However, + # for production apps we strongly suggest only using + case_name = metadata["accessionNumber"] + block_name = metadata["block"]["displayName"] + stain_name = metadata["staining"]["displayName"] + stable_slide_id = hashlib.sha1( + f"{metadata['seriesInstanceUid']}".encode("UTF-8") + ).hexdigest()[:10] + + # write metadata to a requests folder + data_folder = Path( + f"./data/requests/{case_name}/{block_name}-{stain_name}-{stable_slide_id}" + ) + data_folder.mkdir(parents=True, exist_ok=True) + + metadata_filename = data_folder / "metadata.json" + with open(metadata_filename, "w") as file: + json.dump(metadata, file) + + save_filename = ( + data_folder / f"request_user-{datetime.now().strftime('%Y%m%d%H%M%S')}.json" + ) + with open(save_filename, "w") as file: + json.dump(data, file) + + # also write a file in a flat queue folder, this folder will represent + # the "active" queue and the data folder can be a larger repository of all requests + queue_folder = Path("./data/queue") + queue_folder.mkdir(parents=True, exist_ok=True) + slide_queue_file = ( + queue_folder / f"{case_name}-{block_name}-{stain_name}-{stable_slide_id}.txt" + ) + slide_queue_file.write_text( + f"../../{save_filename}\n" + ) # persist a "link" to the most recent metadata + + # prepare to store a progress label visible to users + text = "analysis queued" + max_y = metadata["imageSize"]["height"] / metadata["imageSize"]["width"] + store_data = { + "slideId": data["slideId"], + "displayResult": text, # text as shown in the annotation list (L) + "displayProperties": { + # table-style properties shown when the annotation is selected + "Progress": "0 %" + }, + "applicationVersion": __version__, + "data": { + "context": {}, + "result": { + "type": "primitive", + "content": { + "style": { + "fillStyle": None, + "size": None, + "strokeStyle": "#FFA500", + }, + "polygons": [ + { + "points": [ + {"x": 0.0, "y": 0.0}, + {"x": 1.0, "y": 0.0}, + {"x": 1.0, "y": max_y}, + {"x": 0.0, "y": max_y}, + ] + } + ], + "labels": [ + # place label at the top center + {"location": {"x": 0.5, "y": 0.0}, "label": text} + ], + }, + }, + }, + } + + # check if there is already an app result from our app for this slide + # since apps cannot DELETE their own results, we modify the existing one to avoid + # creating a new one every time + r = api.get(f"applications/{data['applicationId']}/results/slide/{data['slideId']}") + r.raise_for_status() + existing_annots = r.json() + if len(existing_annots) > 0: + latest_annot = existing_annots[-1] + latest_annot.update(store_data) + response = api.put( + f"applications/{data['applicationId']}/results/{latest_annot['id']}", + json=latest_annot, + ) + else: + response = api.post( + f"applications/{data['applicationId']}/results/", json=store_data + ) + response.raise_for_status() + # the response we get back is in a suitable format for passing back to the caller + return json_resp(response.json()) + + +def app_delete(data): + """result has been deleted by the user, and our app is informed""" + # do not intervene (will get the result deleted) + return json_resp({}) + + +# ============================================================ +# below code is to support running this through ./webserver.py +# ============================================================ + + +# set default exception handler +def defaultHandler(e): + code = 500 + if hasattr(e, "code"): + code = e.code + print("--- error ---") + print("ERROR:", str(e)) + traceback.print_tb(e.__traceback__) + return json.dumps({"error": str(e)}), code + + +app.config["TRAP_HTTP_EXCEPTIONS"] = True +app.register_error_handler(Exception, defaultHandler) + +if __name__ == "__main__": + app.run(port=BIND_PORT, debug=True) diff --git a/examples/python/ia_wholeslide/src/dpat_wholeslide/worker.py b/examples/python/ia_wholeslide/src/dpat_wholeslide/worker.py new file mode 100755 index 0000000..acddac0 --- /dev/null +++ b/examples/python/ia_wholeslide/src/dpat_wholeslide/worker.py @@ -0,0 +1,423 @@ +#!/usr/bin/env python +import io +import os +import json +import sys + +from pathlib import Path +import time + +import PIL # pip install pillow +import PIL.Image + +import click +from click import secho +from requests_toolbelt import MultipartDecoder +from tqdm import tqdm + +from dpat_wholeslide.version import __version__ +from dpat_wholeslide.dzidesc import DziDescription +from dpat_wholeslide.utils import requests_session_from_callbackinfo +from dpat_wholeslide.locks import lock_release, lock_try_acquire + + +# %% + +# -------------------------------------------- +# Common +# -------------------------------------------- + + +def latest_request_data(folder_path): + """ + Given a slide folder path, locate the latest request data file and return its contents as a dict. + """ + latest_file = sorted(folder_path.glob("request*.json")) + if not latest_file: + return None + latest_file = latest_file[-1] + return json.loads(latest_file.read_text()) + + +def session_from_folder(folder_path): + """ + Given a slide folder path, locate the latest request data file and return a requests Session + together with the request data. + """ + req = latest_request_data(folder_path) + if not req: + raise Exception(f"no user request-json found in '{folder_path}'") + api = requests_session_from_callbackinfo(req["callbackInfo"]) + return api, req + + +def download_thumbnail(folder_path): + """ + Download a thumbnail for the given slide and persist in the slide folder as 'thumbnail.jpg'. + + Examplifies using the tile-based (Deep Zoom Image (DZI) pyramid) API calls. + """ + folder_path = Path(folder_path) + secho(f"downloading thumbnail for '{folder_path}'") + # - locate latest request_user file + api, req = session_from_folder(folder_path) + + # request image metadata + # we re-download metadata even though its in theory persisted in req already + # (for clarity) + slide_id = req["slideId"] + metadata = api.get(f"slides/{slide_id}/info?scope=extended&includePHI=false").json() + # DziDescription is a helper class to manage Deep Zoom Image (DZI) pyramid logic, + # useful when requesting tiles from the Sectra DPAT IA-API. + dzi = DziDescription( + metadata["imageSize"]["width"], + metadata["imageSize"]["height"], + tile_size=metadata["tileSize"]["width"], + tile_overlap=0, + resolution=metadata["micronsPerPixel"], + ) + wanted_mpp = 64.0 # this is microns per pixel, suitable for a thumbnail + (lvl_dzi, mpp_at_level, mpp_diff_f) = dzi.level_at_mpp( + wanted_mpp, always_smaller=True + ) + # prepare a blank image to paste the tiles into + dst_img = PIL.Image.new("RGB", (lvl_dzi.width(), lvl_dzi.height()), color=(0, 0, 0)) + # iterate over all tiles in the level and download them + for tiledesc in tqdm( + lvl_dzi.tiles_for_level(), + desc="downloading thumbnail tiles", + total=lvl_dzi.n_tiles(), + ): + # This is the Sectra DPAT IA-API endpoint for downloading tiles + # GET /images/_files//_[_].[?opticalPath=] + img = io.BytesIO( + api.get( + f"images/{slide_id}_files/{tiledesc.tile.level}/{tiledesc.tile.col}_{tiledesc.tile.row}_0.jpg" + ).content + ) + img_pil = PIL.Image.open(img).convert("RGB") + img_cropped = img_pil.crop( + ( + tiledesc.crop.left, + tiledesc.crop.top, + tiledesc.crop.right, + tiledesc.crop.bottom, + ) + ) + dst_img.paste( + img_cropped, box=(int(tiledesc.place_point.x), int(tiledesc.place_point.y)) + ) + # save the thumbnail to disk + dst_filepath = folder_path / "thumbnail.jpg" + dst_img.save(dst_filepath) + secho(f"wrote thumbnail to '{dst_filepath}'") + + # - download slide label image (NOTE: might contain PHI!) + r = api.get(f"slides/{slide_id}/label") + r.raise_for_status() + if r.status_code == 204: + secho("no label image stored for this slide") + else: + img = io.BytesIO(r.content) + img_pil = PIL.Image.open(img).convert("RGB") + dst_label_filepath = folder_path / "label.jpg" + img_pil.save(dst_label_filepath) + secho(f"wrote label image to '{dst_label_filepath}'") + secho("done") + + +def set_progress(api, req, text, progress_percent): + """ + Update the progress text for the latest result (annotation) of the slide described in req. + + if text is None, will use a template like "analysis, progress {} %" + """ + new_text = text + if not new_text: + new_text = "analysis, progress {} %" + if "{}" in new_text: + new_text = new_text.format(progress_percent) + + # TODO: use this code in webserver.py as well (currently its duplicated) + # TODO: seems this could be a more generic upsert operation for results + r = api.get(f"slides/{req['slideId']}/info?scope=extended&includePHI=false") + r.raise_for_status() + metadata = r.json() + max_y = metadata["imageSize"]["height"] / metadata["imageSize"]["width"] + + store_data = { + "slideId": req["slideId"], + "displayResult": new_text, # text as shown in the annotation list (L) + "displayProperties": { + # table-style properties shown when the annotation is selected + "Progress": f"{progress_percent} %" + }, + "applicationVersion": __version__, + "data": { + "context": {}, + "result": { + "type": "primitive", + "content": { + "style": { + "fillStyle": None, + "size": None, + "strokeStyle": "#FFA500", + }, + "polygons": [ + { + "points": [ + {"x": 0.0, "y": 0.0}, + {"x": 1.0, "y": 0.0}, + {"x": 1.0, "y": max_y}, + {"x": 0.0, "y": max_y}, + ] + } + ], + "labels": [ + # place label at the top center + {"location": {"x": 0.5, "y": 0.0}, "label": new_text} + ], + }, + }, + }, + } + + # check if there is already an app result from our app for this slide + r = api.get(f"applications/{req['applicationId']}/results/slide/{req['slideId']}") + r.raise_for_status() + existing_annots = r.json() + if len(existing_annots) > 0: + latest_annot = existing_annots[-1] + old_text = latest_annot["displayResult"] + latest_annot.update(store_data) + secho(f" updating '{old_text}' -> '{new_text}'") + response = api.put( + f"applications/{req['applicationId']}/results/{latest_annot['id']}", + json=latest_annot, + ) + else: + secho(f" adding new '{new_text}'") + response = api.post( + f"applications/{req['applicationId']}/results/", json=store_data + ) + response.raise_for_status() + + +def download_wsi(folder): + """ + Download the WSI and persist in ./wsi_files/ beneath the slide folder. + """ + folder_path = Path(folder) + # - locate latest request_user file + api, req = session_from_folder(folder_path) + slide_id = req["slideId"] + + secho(f"downloading WSI for '{folder_path}'") + r = api.get(f"slides/{slide_id}/files", stream=True) + + # TODO: the MultipartDecoder in requests-toolbelt reads the entire r.content + # into memory, which means we need to rewrite this to use a custom implementation + if r.headers["Content-Type"].startswith("multipart/related"): + # multiple files + decoder = MultipartDecoder.from_response(r, "utf-8") + for r_part in decoder.parts: + # take all keys in r_part.headers and convert them from byte to str + headers = { + k.decode("utf-8"): v.decode("utf-8") for k, v in r_part.headers.items() + } + filename = ( + headers["Content-Disposition"].split("filename=")[1].strip('""') + + ".dcm" + ) + dest_path = folder_path / f"wsi_files/{filename}" + if not dest_path.exists(): + dest_path.parent.mkdir(exist_ok=True, parents=True) + # we can safely write the entire content to disk here + # because it is already in memory + with open(dest_path, "wb") as f: + f.write(r_part.content) + print(f"wsi saved to '{dest_path}'") + else: + print(f"file already existed, ignored: '{dest_path}'") + else: + # application/octet-stream -- single file + filename = r.headers["Content-Disposition"].split("filename=")[1].strip('""') + tmp_path = folder_path / f"wsi_files/{filename}.part" + dest_path = folder_path / f"wsi_files/{filename}" + if not dest_path.exists(): + print("downloading", dest_path) + dest_path.parent.mkdir(exist_ok=True, parents=True) + with open(tmp_path, "wb") as f: + # configure tqdm to output download speed + sbar = tqdm( + unit="B", ascii=True, unit_scale=True, desc="downloading wsi" + ) + # stream chunks and write to disk + for chunk in r.iter_content(chunk_size=1024 * 1024): + sbar.update(len(chunk)) + f.write(chunk) + tmp_path.rename(dest_path) + print(f"done, wsi saved to '{dest_path}'") + else: + print(f"file already exists: '{dest_path}'") + + +def process_single(folder): + folder_path = Path(folder) + # - locate latest request_user file + api, req = session_from_folder(folder_path) + set_progress(api, req, None, 10) + + # download thumbnail + thumbnail_path = folder_path / "thumbnail.jpg" + if not thumbnail_path.exists(): + download_thumbnail(folder_path) + set_progress(api, req, None, 20) + + # - download WSI + wsi_folder_path = folder_path / "wsi_files" + if len(list(wsi_folder_path.glob("*"))) == 0: + download_wsi(folder_path) + set_progress(api, req, None, 40) + + # calculate something complicated + secho("doing some complicated analysis") + time.sleep(2) + set_progress(api, req, None, 60) + time.sleep(2) + set_progress(api, req, None, 80) + time.sleep(2) + set_progress(api, req, None, 100) + + # - save final result + metadata = api.get( + f"slides/{req['slideId']}/info?scope=extended&includePHI=false" + ).json() + max_y = metadata["imageSize"]["height"] / metadata["imageSize"]["width"] + text = "ANSWER: 42" + + store_data = { + "slideId": req["slideId"], + "displayResult": text, # text as shown in the annotation list (L) + "displayProperties": {}, + "applicationVersion": __version__, + "data": { + "context": {}, + "result": { + "type": "primitive", + "content": { + "style": { + "fillStyle": None, + "size": None, + "strokeStyle": "#FFA500", + }, + "polygons": [ + { + "points": [ + {"x": 1 * (1.0 / 3), "y": 1 * (max_y / 3)}, + {"x": 2 * (1.0 / 3), "y": 1 * (max_y / 3)}, + {"x": 2 * (1.0 / 3), "y": 2 * (max_y / 3)}, + {"x": 1 * (1.0 / 3), "y": 2 * (max_y / 3)}, + ] + } + ], + "labels": [ + # place label at the center + { + "location": {"x": 0.5, "y": max_y / 2.0}, + "label": text, + } + ], + }, + }, + }, + } + + # check for existing result + r = api.get(f"applications/{req['applicationId']}/results/slide/{req['slideId']}") + existing_annots = r.json() + if len(existing_annots) > 0: + # update existing resulti nstead + latest_annot = existing_annots[-1] + latest_annot.update(store_data) + response = api.put( + f"applications/{req['applicationId']}/results/{latest_annot['id']}", + json=latest_annot, + ) + else: + response = api.post( + f"applications/{req['applicationId']}/results/", json=store_data + ) + response.raise_for_status() + secho("saved final result. done") + + +# -------------------------------------------- +# CLI Commands +# -------------------------------------------- + + +@click.group() +def main(): + pass + + +# ============================================ +# Process single case +# ============================================ +@main.command(name="process", help="process single slide") +@click.argument("slide_folder") +def cli_process_single(slide_folder): + """ + Process a single slide. Processing will download thumbnail, WSI and compute a result. + """ + return process_single(slide_folder) + + +# ============================================ +# watch -- e.g. act as Queue Controller +# ============================================ +@main.command(name="watch", help="start monitoring for WSI processing requests") +@click.argument("queue_folder") +def cli_watch(queue_folder): + """ + Start a persistent monitoring process that acts when user requests are made. + """ + secho(f"starting watch loop, monitoring '{queue_folder}'") + secho("Press CTRL-C to stop.") + while True: + # list all .txt files in queue_folder sorted by modification time (oldest first) + for queue_file in sorted( + Path(queue_folder).glob("*.txt"), key=os.path.getmtime + ): + queue_file_lock = queue_file.with_suffix(".lock") + queue_lock = lock_try_acquire(str(queue_file_lock)) + if queue_lock is None: + # lock not acquired, skip this file + continue + + # lock acquired, process the file + try: + 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