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tidy up

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This commit is contained in:
Ross
2024-12-09 11:13:46 +00:00
parent 8aae29f3e8
commit 66b4fffb7b
10 changed files with 227 additions and 548 deletions
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.gitignore
+2
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@@ -12,3 +12,5 @@ dist
test/*
*.build
C:/* # Windows paths on linux
anon2/anon_gui.spec
-44
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@@ -1,44 +0,0 @@
# -*- mode: python ; coding: utf-8 -*-
block_cipher = None
a = Analysis(
['anon_gui.py'],
pathex=[],
binaries=[],
datas=[],
hiddenimports=[],
hookspath=[],
hooksconfig={},
runtime_hooks=[],
excludes=[],
win_no_prefer_redirects=False,
win_private_assemblies=False,
cipher=block_cipher,
noarchive=False,
)
pyz = PYZ(a.pure, a.zipped_data, cipher=block_cipher)
exe = EXE(
pyz,
a.scripts,
a.binaries,
a.zipfiles,
a.datas,
[],
name='anon_gui',
debug=False,
bootloader_ignore_signals=False,
strip=False,
upx=True,
upx_exclude=[],
runtime_tmpdir=None,
console=False,
disable_windowed_traceback=False,
argv_emulation=False,
target_arch=None,
codesign_identity=None,
entitlements_file=None,
)
anon_gui.cmd
-6
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@@ -1,6 +0,0 @@
@echo off
rem This script was created by Nuitka to execute 'anon_gui.exe' with Python DLL being found.
set PATH=C:\PROGRA~1\PYTHON~1;%PATH%
set PYTHONHOME=C:\Program Files\Python311
"%~dp0anon_gui.exe" %*
anon_gui.exe
BIN
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Binary file not shown.
anon_gui.py
+3
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@@ -1,3 +1,6 @@
# This is a legacy app written in wxPython
# Whilst it works (or did prior to any API changes)
# it was not particularly well designed
from collections import defaultdict
import json
import os
client.py
-65
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@@ -1,65 +0,0 @@
import typer
import requests
app = typer.Typer()
from bs4 import BeautifulSoup
# client.py
LOGIN_URL = "https://www.penracourses.org.uk/accounts/login"
# ADD_URL = 'http://localhost/add'
@app.command()
def login(user: str, password: str):
rqst = requests.session()
rsp = rqst.get(LOGIN_URL)
token = BeautifulSoup(rsp.content, "html.parser").find("input").attrs["value"]#, attr={"name": "csrfmiddlewaretoken"}).attrs("value")
#token = rsp.cookies["csrftoken"]
#header = {"X-CSRFToken": token}
#cookies = {"csrftoken": token}
data = {
"username": user,
"password": password,
"csrfmiddlewaretoken": token,
"next": "/",
}
print(data)
rqst.headers["Referer"] = LOGIN_URL
rsp = rqst.post(
LOGIN_URL,
data=data,
#headers=header,
#cookies=cookies
)
soup = BeautifulSoup(rsp.content, "html.parser")
print(token)
print(rqst.headers)
print(rqst.cookies)
login_success = False
if soup.find("button") and soup.find("button").find(string="Login"):
print("login fail")
pass
else:
print("login success")
login_success = True
#print(rqst.headers)
#print(rsp.content)
#new = rqst.get(
# "https://www.penracourses.org.uk/api/atlas/get_cases_user"
#)
#print(new)
#print(new.content)
if __name__ == "__main__":
app()
nice.py
+186 -175
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@@ -1,20 +1,17 @@
#!/usr/bin/env python3
import asyncio
import pynng
# asyncio.set_event_loop_policy(asyncio.WindowsSelectorEventLoopPolicy())
from collections import defaultdict
from pathlib import Path
from bs4 import BeautifulSoup
from local_file_picker import local_file_picker
from nicegui import ui, app, html, run, Client, native
from datetime import datetime
import zmq
import zmq.asyncio
from loguru import logger
import sys
@@ -26,10 +23,9 @@ import time
from multiprocessing import Manager, Queue, freeze_support
import watchfiles
from functools import partial
from local_file_picker import local_file_picker
from local_folder_picker import local_folder_picker
from typing import Optional
@@ -39,29 +35,7 @@ from fastapi.responses import RedirectResponse
from starlette.middleware.base import BaseHTTPMiddleware
import typer
#typer_app = typer.Typer()
#logger.add(sys.stderr, format="{time} {level} {message}", filter="my_module", level="INFO")
#async def pick_file() -> None:
# result = await local_file_picker('~', multiple=True)
# ui.notify(f'You chose {result}')
# ui.html("<h2>Uploader tool</h2>")
#
# ui.chat_message(f'{result}!',
# name='Robot',
# stamp='now',
# avatar='https://robohash.org/ui')
#
#
#@ui.page('/')
#def index():
# ui.html("<h2>Uploader tool</h2>")
# ui.button('Choose file', on_click=pick_file, icon='folder')
NATIVE = False
SOCKET_PATH = 'tcp://localhost:9976'
SOCKET_PATH = "tcp://localhost:9976"
WORK_DIR = Path("C:/uploader")
@@ -83,6 +57,7 @@ LOGGED_IN_USER = "None"
REFRESH_TRIGGERED = True
SHUTDOWN = False
DELETE_FILES_ON_UPLOAD = True
@@ -98,8 +73,6 @@ if DEBUG:
rqst = None
use_zmq = False
use_nng = True
loaded_files: dict = {}
loaded_series = defaultdict(list)
loaded_series_data = {}
@@ -107,55 +80,6 @@ uploaded_files: dict = {}
duplicate_series = set()
if use_zmq:
context = zmq.asyncio.Context()
socket = context.socket(zmq.PULL)
#socket.bind('tcp://localhost:5575')
try:
socket.bind(SOCKET_PATH)
except zmq.error.ZMQError as e:
logger.debug("send reload")
socket = context.socket(zmq.PUSH)
socket.connect(SOCKET_PATH)
socket.send_string("loaded")
sys.exit(0)
#app.shutdown()
poller = zmq.asyncio.Poller()
poller.register(socket, zmq.POLLIN)
async def read_loop() -> None:
while not app.is_stopped:
events = await poller.poll()
if socket in dict(events):
data = await socket.recv()
msg = data.decode()
logger.debug(f'Received msg {msg}')
match msg:
case "loaded":
for client in Client.instances.values():
if not client.has_socket_connection:
continue
with client:
ui.notify("Export done", color='positive')
global REFRESH_TRIGGERED
REFRESH_TRIGGERED = True
logger.debug("loaded")
#with updates:
# ui.item(f"{datetime.now().strftime('%H:%M:%S')} - {msg}")
#logger.debug("loaded")
#load_files_start()
case _:
logger.error("invalid message")
if use_nng:
async def read_nng_messages():
print("start nng")
try:
@@ -164,14 +88,14 @@ if use_nng:
while not app.is_stopped:
msg = await sub.arecv_msg()
data = msg.bytes.decode()
logger.debug(f'Received msg {data}')
logger.debug(f"Received msg {data}")
match data:
case "loaded":
for client in Client.instances.values():
if not client.has_socket_connection:
continue
with client:
ui.notify("Export done", color='positive')
ui.notify("Export done", color="positive")
global REFRESH_TRIGGERED
REFRESH_TRIGGERED = True
logger.debug("loaded")
@@ -181,14 +105,19 @@ if use_nng:
logger.debug("Address in use")
with pynng.Pair0(dial=SOCKET_PATH) as sub:
await sub.asend(b"loaded")
sys.exit(0)
# Trigger shutdown from in the async loop
# This shouldn't be necessary
global SHUTDOWN
SHUTDOWN = True
return
# asyncio.create_task(read_nng_messages())
anonymizer = Anonymizer(ANON_PATH)
async def upload_files_start(progress, upload_queue):
global uploaded_files, duplicate_series
progress.visible = True
@@ -197,32 +126,49 @@ async def upload_files_start(progress, upload_queue):
progress.visible = False
if results:
new_uploaded_files, upload_file_list, duplicate_file_list, failed, duplicate_series = results
(
new_uploaded_files,
upload_file_list,
duplicate_file_list,
failed,
duplicate_series,
) = results
else:
ui.notify("No files to upload", color="negative")
return
uploaded_files.update(new_uploaded_files)
ui.notify(f"Uploaded {len(upload_file_list)} files", color='positive')
ui.notify(f"Duplicate {len(duplicate_file_list)} files", color='warning')
ui.notify(f"Failed {len(failed)} files", color='negative')
ui.notify(f"Uploaded {len(upload_file_list)} files", color="positive")
if duplicate_file_list:
ui.notify(f"Duplicate {len(duplicate_file_list)} files", color="warning")
if failed:
ui.notify(f"Failed {len(failed)} files", color="negative")
if DELETE_FILES_ON_UPLOAD:
clear_anonymized_files()
loaded_series_ui.refresh()
loaded_files_ui.refresh()
uploaded_files_ui.refresh()
async def load_files_start(progress_bar, queue, custom_path=None):
logger.debug("load files start")
global loaded_files, loaded_series, loaded_series_data
progress_bar.visible = True
new_loaded_files, new_loaded_series, new_loaded_series_data = await run.cpu_bound(load_files, queue, custom_path)
new_loaded_files, new_loaded_series, new_loaded_series_data = await run.cpu_bound(
load_files, queue, custom_path
)
for client in Client.instances.values():
if not client.has_socket_connection:
continue
with client:
ui.notify(f"Files loaded: {len(new_loaded_files)}, [Series: {len(new_loaded_series)}] ", color="positive")
loaded_files.update(new_loaded_files)
loaded_series.update(new_loaded_series)
@@ -233,26 +179,33 @@ async def load_files_start(progress_bar, queue, custom_path=None):
loaded_series_ui.refresh()
loaded_files_ui.refresh()
async def reload_anonymized_start(progress_bar, queue):
global loaded_files, loaded_series, loaded_series_data
progress_bar.visible = True
loaded_files, loaded_series, loaded_series_data = await run.cpu_bound(reload_anonymized, queue)
loaded_files, loaded_series, loaded_series_data = await run.cpu_bound(
reload_anonymized, queue
)
progress_bar.visible = False
ui.notify(f"Files reloaded: {len(loaded_files)}, [Series: {len(loaded_series)}] ", color="positive")
# load_series_view(loaded_series, loaded_series_data)
loaded_series_ui.refresh()
loaded_files_ui.refresh()
@ui.refreshable
def user_info_ui():
global LOGGED_IN_USER
user_label = ui.label(f"User: {LOGGED_IN_USER}")
# user_label.bind_visibility_from(globals(), "LOGIN_SUCCESS")
@ui.refreshable
def loaded_series_ui() -> None:
global loaded_series, loaded_series_data
series_title = ui.label('Series to upload').classes("text-h3")
series_title = ui.label("Series to upload").classes("text-h3")
series_title.visible = False
series = ui.row()
@@ -271,9 +224,10 @@ def loaded_series_ui() -> None:
if loaded_series:
series_title.visible = True
@ui.refreshable
def loaded_files_ui() -> None:
with ui.expansion('Loaded files', icon='drive_folder_upload').classes('w-full'):
with ui.expansion("Loaded files", icon="drive_folder_upload").classes("w-full"):
ui.label(f"Items: {len(loaded_files)}")
with ui.list():
for file, data in loaded_files.items():
@@ -282,15 +236,21 @@ def loaded_files_ui() -> None:
@ui.refreshable
def uploaded_files_ui() -> None:
with ui.expansion('Uploaded files', icon='file_upload').classes('w-full'):
with ui.expansion("Uploaded files", icon="file_upload").classes("w-full"):
ui.label(f"Items: {len(uploaded_files)}")
with ui.list():
for series in duplicate_series:
ui.item(f"Duplicate series: {series}", on_click=lambda: ui.navigate.to(f'{BASE_SITE_URL}{series}', new_tab=True)).classes("text-red-500")
ui.item(
f"Duplicate series: {series}",
on_click=lambda: ui.navigate.to(
f"{BASE_SITE_URL}{series}", new_tab=True
),
).classes("text-red-500")
with ui.list():
for file, data in uploaded_files.items():
ui.item(f"{file} - {data}")
def load_files(q: Queue, src_path: Path | None = None):
loaded_files: dict = {}
loaded_series = defaultdict(list)
@@ -314,10 +274,17 @@ def load_files(q: Queue, src_path: Path | None = None):
# with processed_files:
# ui.item(f"{datetime.now().strftime('%H:%M:%S')} - {file.name} -> {output_file.name}")
loaded_files[output_file] = (dataset.StudyDescription, dataset.SeriesDescription, str(dataset.SeriesInstanceUID))
loaded_files[output_file] = (
dataset.StudyDescription,
dataset.SeriesDescription,
str(dataset.SeriesInstanceUID),
)
loaded_series[dataset.SeriesInstanceUID].append(output_file)
loaded_series_data[dataset.SeriesInstanceUID] = (dataset.StudyDescription, dataset.SeriesDescription)
loaded_series_data[dataset.SeriesInstanceUID] = (
dataset.StudyDescription,
dataset.SeriesDescription,
)
q.put_nowait((n + 1) / to_process_len)
@@ -326,7 +293,6 @@ def load_files(q: Queue, src_path: Path | None = None):
return loaded_files, loaded_series, loaded_series_data
def reload_anonymized(q: Queue):
loaded_files = {}
loaded_series = defaultdict(list)
@@ -334,20 +300,25 @@ def reload_anonymized(q: Queue):
# processed_files.clear()
to_process = list(ANON_PATH.glob("**/*.dcm"))
to_process_len = len(to_process)
for n, file in enumerate(to_process):
with pydicom.dcmread(file) as dataset:
loaded_files[file] = (dataset.StudyDescription, dataset.SeriesDescription, str(dataset.SeriesInstanceUID))
loaded_files[file] = (
dataset.StudyDescription,
dataset.SeriesDescription,
str(dataset.SeriesInstanceUID),
)
loaded_series[dataset.SeriesInstanceUID].append(file)
loaded_series_data[dataset.SeriesInstanceUID] = (dataset.StudyDescription, dataset.SeriesDescription)
loaded_series_data[dataset.SeriesInstanceUID] = (
dataset.StudyDescription,
dataset.SeriesDescription,
)
# with processed_files:
# ui.item(f"{datetime.now().strftime('%H:%M:%S')} - {file.name} -> Reloaded")
q.put_nowait(f"{(n + 1) / to_process_len * 100:.0f}%")
logger.debug(file)
@@ -360,6 +331,7 @@ def reload_anonymized(q: Queue):
return loaded_files, loaded_series, loaded_series_data
def clear_anonymized_files():
for file in ANON_PATH.iterdir():
if file.is_file():
@@ -369,6 +341,7 @@ def clear_anonymized_files():
return
def upload_files(q, rqst):
# global rqst#, uploaded_files
@@ -387,7 +360,6 @@ def upload_files(q, rqst):
files_to_upload[i : i + n] for i in range(0, len(files_to_upload), n)
]
upload_file_list = []
duplicate_file_list = []
failed = []
@@ -447,26 +419,28 @@ def upload_files(q, rqst):
for f in failed:
uploaded_files[f] = "failed"
return uploaded_files, upload_file_list, duplicate_file_list, failed, duplicate_series
return (
uploaded_files,
upload_file_list,
duplicate_file_list,
failed,
duplicate_series,
)
@ui.page('/login')
@ui.page("/login")
def login() -> Optional[RedirectResponse]:
dark = ui.dark_mode()
dark.enable()
def try_login() -> None: # local function to avoid passing username and password as arguments
logger.debug(username.value)
#if passwords.get(username.value) == password.value:
# app.storage.user.update({'username': username.value, 'authenticated': True})
# ui.navigate.to(app.storage.user.get('referrer_path', '/')) # go back to where the user wanted to go
#else:
# ui.notify('Wrong username or password', color='negative')
def try_login() -> (
None
): # local function to avoid passing username and password as arguments
# Because I haven't gotten around to implementing a proper login system yet
# we just log in via requests and store teh session in the global rqst variable
user = username.value
pw = password.value
@@ -475,7 +449,7 @@ def login() -> Optional[RedirectResponse]:
try:
rsp = rqst.get(LOGIN_URL)
except requests.exceptions.ConnectionError:
ui.notify('Connection error!', color='negative')
ui.notify("Connection error!", color="negative")
return
token = (
@@ -520,88 +494,91 @@ def login() -> Optional[RedirectResponse]:
rqst.headers["X-CSRFToken"] = token
print(rqst.headers)
print(rqst.cookies)
new = rqst.get(f"{BASE_SITE_URL}/accounts/api/atlas/get_cases_user")
if LOGIN_SUCCESS:
ui.notify('Logged in!', color='positive')
ui.notify("Logged in!", color="positive")
ui.navigate.to("/")
#login_button.visible = False
pass
#self.parent.upload_button.Enable()
#self.parent.login_button.Hide()
#self.parent.panel.Layout()
#self.Destroy()
# self.parent.login_button.SetBackgroundColour(wx.BLUE)
# self.parent.login_button.SetForegroundColour(wx.WHITE)
else:
ui.notify('Wrong username or password', color='negative')
pass
#self.login_fail()
ui.notify("Wrong username or password", color="negative")
# if app.storage.user.get('authenticated', False):
# return RedirectResponse('/')
with ui.card().classes('absolute-center'):
username = ui.input('Username').on('keydown.enter', try_login)
password = ui.input('Password', password=True, password_toggle_button=True).on('keydown.enter', try_login)
ui.button('Log in', on_click=try_login)
with ui.card().classes("absolute-center"):
username = ui.input("Username").on("keydown.enter", try_login)
password = ui.input("Password", password=True, password_toggle_button=True).on(
"keydown.enter", try_login
)
with ui.row():
ui.button("Log in", on_click=try_login)
ui.button("Cancel", on_click=lambda: ui.navigate.to("/"), color="red")
return None
@ui.page('/')
def main_page():
@ui.page("/")
def main_page():
async def watch_for_shutdown():
global SHUTDOWN
while not app.is_stopped:
if SHUTDOWN:
logger.debug("Trigger app shutdown")
app.shutdown()
await asyncio.sleep(1)
asyncio.create_task(watch_for_shutdown())
dark = ui.dark_mode()
dark.enable()
ui.page_title('Uploader tool')
ui.label('Uploader tool').classes("text-h2")
ui.page_title("Uploader tool")
ui.label("Uploader tool").classes("text-h2")
user_info_ui()
login_button = ui.button("LOGIN", on_click=lambda: ui.navigate.to("/login"))
login_button.bind_visibility_from(globals(), "LOGIN_SUCCESS", backward=lambda v: not v)
login_button.bind_visibility_from(
globals(), "LOGIN_SUCCESS", backward=lambda v: not v
)
updates = ui.list()
loaded_series_ui()
# typer_app()
# Create a queue to communicate with the heavy computation process
queue = Manager().Queue()
# Update the progress bar on the main process
ui.timer(0.1, callback=lambda: progressbar.set_value(queue.get() if not queue.empty() else progressbar.value))
ui.timer(
0.1,
callback=lambda: progressbar.set_value(
queue.get() if not queue.empty() else progressbar.value
),
)
# Create a queue to communicate with the heavy computation process
upload_queue = Manager().Queue()
# Update the progress bar on the main process
ui.timer(0.1, callback=lambda: upload_progressbar.set_value(upload_queue.get() if not upload_queue.empty() else upload_progressbar.value))
ui.timer(
0.1,
callback=lambda: upload_progressbar.set_value(
upload_queue.get() if not upload_queue.empty() else upload_progressbar.value
),
)
upload_progress = ui.row().classes("w-full place-content-center bg-blue-900")
with upload_progress:
ui.label("Uploading files")
upload_progressbar = ui.linear_progress(value=0).props('instant-feedback')
upload_progressbar = ui.linear_progress(value=0).props("instant-feedback")
upload_progress.visible = False
upload_button = ui.button("Upload", on_click=partial(upload_files_start, upload_progress, upload_queue))
upload_button = ui.button(
"Upload", on_click=partial(upload_files_start, upload_progress, upload_queue)
)
upload_button.bind_visibility_from(globals(), "LOGIN_SUCCESS")
anon_progress = ui.row().classes("w-full place-content-center bg-blue-900")
with anon_progress:
ui.label("Anonymizing files")
progressbar = ui.linear_progress(value=0).props('instant-feedback')
progressbar = ui.linear_progress(value=0).props("instant-feedback")
anon_progress.visible = False
async def load_files_from_folder() -> None:
@@ -612,14 +589,19 @@ def main_page():
await load_files_start(anon_progress, queue, folder)
# return dir
else:
ui.notify("No folder selected", color='negative')
ui.notify("No folder selected", color="negative")
with ui.expansion('Extra', icon='build').classes('w-full'):
ui.button("Load files", on_click=partial(load_files_start, anon_progress, queue))
with ui.expansion("Extra", icon="build").classes("w-full"):
ui.button(
"Load files", on_click=partial(load_files_start, anon_progress, queue)
)
ui.button("Load files from folder", on_click=load_files_from_folder)
ui.button("Reload anon", on_click=partial(reload_anonymized_start, anon_progress, queue))
ui.button(
"Reload anon",
on_click=partial(reload_anonymized_start, anon_progress, queue),
)
with ui.expansion('File status', icon='view_list').classes('w-full'):
with ui.expansion("File status", icon="view_list").classes("w-full"):
loaded_files_ui()
uploaded_files_ui()
@@ -631,13 +613,13 @@ def main_page():
ui.label(f"Export path: {EXPORT_PATH}")
ui.label(f"Process path: {PROCESS_PATH}")
ui.label(f"Anon path: {ANON_PATH}")
ui.button("Clear anon path", on_click=clear_anonymized_files).tooltip("Delete all files in ANON_PATH")
ui.button("Clear anon path", on_click=clear_anonymized_files).tooltip(
"Delete all files in ANON_PATH"
)
ui.button("Shutdown", on_click=app.shutdown)
ui.notify("Welcome to the uploader tool", color='positive')
def shutdown_app():
app.shutdown()
ui.run_javascript("window.close()")
async def watch_for_refresh():
global REFRESH_TRIGGERED
@@ -649,29 +631,58 @@ def main_page():
asyncio.create_task(watch_for_refresh())
with ui.dialog() as about_dialog:
with ui.card().classes("absolute-center"):
ui.label("Uploader tool").classes("text-h2")
ui.label("A tool to help upload files to penracourses.org.uk")
ui.image("icon/icon1.png")
ui.label("Version: 0.1")
ui.label("Author: Ross Kruger")
def launch_app(work_dir: Path = typer.Option(WORK_DIR, help="Working directory"), nng: bool = typer.Option(use_nng, help="Use nng")):
global WORK_DIR, EXPORT_PATH, PROCESS_PATH, ANON_PATH, use_nng
ui.button("Close", on_click=about_dialog.close, icon="close", color="secondary")
with ui.footer():
with ui.row():
ui.button("Shutdown", on_click=shutdown_app).props("outline color=white")
ui.button("About", on_click=about_dialog.open).props("outline color=white")
def launch_app(
work_dir: Path = typer.Option(WORK_DIR, help="Working directory"),
nng: bool = typer.Option(True, help="Use nng"),
native_mode: bool = typer.Option(False, help="Use native mode"),
):
global WORK_DIR, EXPORT_PATH, PROCESS_PATH, ANON_PATH
WORK_DIR = work_dir
EXPORT_PATH = WORK_DIR / Path("export/")
PROCESS_PATH = WORK_DIR / Path("to_process/")
ANON_PATH = WORK_DIR / Path("anon/")
logger.error(ANON_PATH)
logger.debug(f"Work dir: {WORK_DIR}")
if nng:
use_nng = True
try:
with pynng.Pair0(listen=SOCKET_PATH) as sub:
pass
except pynng.exceptions.AddressInUse:
logger.debug("Address in use")
with pynng.Pair0(dial=SOCKET_PATH) as sub:
sub.send(b"loaded")
sys.exit(0)
if use_nng:
app.on_startup(read_nng_messages)
app.on_exception(logger.debug)
try:
ui.run(reload=False, show=True, port=native.find_open_port(), native=native_mode, favicon="icon/icon1.ico")
except Exception as e:
logger.error(e)
pass
ui.run(storage_secret="123456", reload=False, show=True, port=native.find_open_port(), native=NATIVE)
if __name__ in {"__main__", "__mp_main__"}:
freeze_support()
typer.run(launch_app)
test_nng.py
-6
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import pynng
with pynng.Pair0(listen='tcp://127.0.0.1:54321') as s1:
with pynng.Pair0(listen='tcp://127.0.0.1:54321') as s2:
pass
uploader.py
-193
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import webview
import time
import sys
from datauri import DataURI
from pathlib import Path
import pydicom
import dicognito.anonymizer
import typer
from typing import List
from watchdog.observers import Observer
# from watchdog.events import LoggingEventHandler
from watchdog.events import PatternMatchingEventHandler
anonymizer = dicognito.anonymizer.Anonymizer()
app = typer.Typer()
def anonymize_file(filepath):
try:
with pydicom.dcmread(filepath) as dataset:
anonymizer.anonymize(dataset)
p = Path(filepath)
new_filename = Path(p.parent, f"{p.stem}_anon{p.suffix}")
dataset.save_as(new_filename)
return new_filename
except:
# Cannot anonymise so just return the same path
return filepath
class PythonJavascriptApi:
def __init__(self):
self.cancel_heavy_stuff_flag = False
def init(self):
response = {"message": "Hello from Python {0}".format(sys.version)}
return response
def sayHelloTo(self, name):
response = {"message": "Hello {0}!".format(name)}
return response
def error(self):
raise Exception("This is a Python exception")
class Watcher:
def __init__(self, window, anonymise: bool) -> None:
self.window = window
self.anonymise = anonymise
def on_created(self, event):
print(f"hey, {event.src_path} has been created!")
path = event.src_path
if self.anonymise:
path = anonymize_file(path)
try:
file_uri = DataURI.from_file(path)
except FileNotFoundError:
print("File deleted...")
return
file_name = Path(path).name
self.injectFile(file_uri, file_name)
def on_deleted(self, event):
print(f"what the f**k! Someone deleted {event.src_path}!")
def on_modified(self, event):
print(f"hey buddy, {event.src_path} has been modified")
def on_moved(self, event):
print(f"ok ok ok, someone moved {event.src_path} to {event.dest_path}")
def injectFile(self, file_uri: DataURI, file_name: str):
current_url = webview.windows[0].get_current_url()
if current_url == "https://www.penracourses.org.uk/rapids/create/":
print(f"inject {file_name}")
self.window.evaluate_js(
f"""
function urltoFile(url, filename, mimeType){{
return (fetch(url)
.then(function(res){{ return res.arrayBuffer(); }})
.then(function(buf){{return new File([buf], filename,{{type:mimeType}});}})
);
}}
$(document).ready(() => {{
//Usage example:
urltoFile('{file_uri}', '{file_name}', '{file_uri.mimetype}')
.then(function(file){{
console.log(file);
//inputs = $("#rapid-form input[type=file][id^=id_images-]");
inputs = extendInputs(1);
console.log(inputs);
el = inputs.get(0);
console.log(el);
let dT = new DataTransfer();
dT.clearData();
dT.items.add(file);
el.files = dT.files;
// Manually fire the change event (qt doesn't seem to...)
$(el).change();
}});
}});
"""
)
@app.command()
def anatomy(filepath: str):
raise NotImplementedError
@app.command()
def rapid(watch_path: Path = "/home/ross/watch", anonymise: bool = True):
api = PythonJavascriptApi()
window = webview.create_window(
"Upload Rapid", "https://www.penracourses.org.uk/rapids/create/", js_api=api
)
# def on_loaded():
# print('DOM is ready')
# current_url = webview.windows[0].get_current_url()
# if current_url == "https://www.penracourses.org.uk/rapids/create/":
# #window.evaluate_js("alert('tent')")
# for file_uri, file_name in uri_name_list:
# #time.sleep(2)
# ## unsubscribe event listener
# #webview.windows[0].loaded -= on_loaded
# #webview.windows[0].load_url('https://google.com')
# window.loaded += on_loaded
# window = upload_rapid(["/home/ross/Downloads/DICOM CT/DICOM CXR/STD1/SER1/CXR.dcm"])
patterns = ["*"]
ignore_patterns = ["*anon*"]
ignore_directories = False
case_sensitive = True
my_event_handler = PatternMatchingEventHandler(
patterns, ignore_patterns, ignore_directories, case_sensitive
)
watcher = Watcher(window, anonymise)
my_event_handler.on_created = watcher.on_created
my_event_handler.on_deleted = watcher.on_deleted
my_event_handler.on_modified = watcher.on_modified
my_event_handler.on_moved = watcher.on_moved
my_observer = Observer()
Path(watch_path).mkdir(parents=True, exist_ok=True)
my_observer.schedule(my_event_handler, watch_path, recursive=True)
my_observer.start()
# try:
# while True:
# time.sleep(1)
# except KeyboardInterrupt:
# my_observer.stop()
# my_observer.join()
webview.start(None, window, debug=True, gui="qt")
# f = "/media/ross/f6200b79-c343-4882-a245-28fc06d43006/Downloads/temp/breasts.jpg"
f = "/home/ross/Downloads/DICOM CT/DICOM CXR/STD1/SER1/CXR.dcm"
if __name__ == "__main__":
app()
zmq-server.py
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#!/usr/bin/env python3
import asyncio
import random
import zmq
import zmq.asyncio
context = zmq.asyncio.Context()
socket = context.socket(zmq.PUSH)
socket.connect('tcp://localhost:5575')
async def send_loop():
#print(f'Sending number {number}')
print("Send hello")
await socket.send_string("loaded")
#await asyncio.sleep(0.1)
print("end")
asyncio.run(send_loop())