ross/uploader
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

numerous improvements

Browse Source
This commit is contained in:
Ross
2024-02-19 11:15:15 +00:00
parent 1e3318dfd6
commit e4c5847fd1
1 changed files with 162 additions and 95 deletions
Download Patch File Download Diff File Expand all files Collapse all files
anon_gui.py
+162 -95
View File
@@ -61,7 +61,6 @@ except ImportError: # if it's not there locally, try the wxPython lib.
import wx.lib.agw.pygauge as PG import wx.lib.agw.pygauge as PG
import wx.lib.agw.thumbnailctrl as TC import wx.lib.agw.thumbnailctrl as TC
import wx.lib.agw.ultimatelistctrl as ULC import wx.lib.agw.ultimatelistctrl as ULC
@@ -192,13 +191,12 @@ def annonymise(
anonymize_file(file, new_filepath) anonymize_file(file, new_filepath)
# progress_dialog.Destroy() # progress_dialog.Destroy()
return new_filepath return new_filepath
def anonymize_file(file: Path, new_filepath: Path): def anonymize_file(file: Path, new_filepath: Path, remove_original: bool = False):
logger.debug(f"Annonymise file, in={file}, out={new_filepath}") logger.debug(f"Annonymise file, in={file}, out={new_filepath}")
# Ensure the output folder exists # Ensure the output folder exists
new_filepath.parents[0].mkdir(parents=True, exist_ok=True) new_filepath.parents[0].mkdir(parents=True, exist_ok=True)
@@ -210,6 +208,9 @@ def anonymize_file(file: Path, new_filepath: Path):
with pydicom.dcmread(file) as dataset: with pydicom.dcmread(file) as dataset:
anonymizer.anonymize(dataset) anonymizer.anonymize(dataset)
dataset.save_as(new_filepath) dataset.save_as(new_filepath)
if remove_original:
os.remove(file)
return dataset, new_filepath return dataset, new_filepath
@@ -298,7 +299,7 @@ class LoginDialog(wx.Dialog):
main_sizer.Add(user_sizer, 0, wx.ALL, 5) main_sizer.Add(user_sizer, 0, wx.ALL, 5)
main_sizer.Add(p_sizer, 0, wx.ALL, 5) main_sizer.Add(p_sizer, 0, wx.ALL, 5)
btn = wx.Button(self, label="Login") btn = wx.Button(self, id=wx.ID_OK, label="Login")
btn.Bind(wx.EVT_BUTTON, self.on_login) btn.Bind(wx.EVT_BUTTON, self.on_login)
main_sizer.Add(btn, 0, wx.ALL | wx.CENTER, 5) main_sizer.Add(btn, 0, wx.ALL | wx.CENTER, 5)
@@ -372,7 +373,7 @@ class LoginDialog(wx.Dialog):
print(new.content) print(new.content)
if self.parent.login_success: if self.parent.login_success:
self.parent.upload_button.Show() self.parent.upload_button.Enable()
self.parent.login_button.Hide() self.parent.login_button.Hide()
self.parent.panel.Layout() self.parent.panel.Layout()
self.Destroy() self.Destroy()
@@ -477,6 +478,7 @@ class AnonGui(wx.App):
clear_files=True, clear_files=True,
clear_files_on_close=True, clear_files_on_close=True,
dev=False, dev=False,
remove_files_on_annonymisation=False,
): ):
self.dir = output_dir self.dir = output_dir
self.input_dir = input_dir self.input_dir = input_dir
@@ -500,6 +502,7 @@ class AnonGui(wx.App):
self.silent_fail = silent_fail self.silent_fail = silent_fail
self.clear_files_on_start = clear_files self.clear_files_on_start = clear_files
self.clear_files_on_close = clear_files_on_close self.clear_files_on_close = clear_files_on_close
self.remove_files_on_annonymisation = remove_files_on_annonymisation
self.rqst = None self.rqst = None
@@ -575,7 +578,7 @@ class AnonGui(wx.App):
self.link_rapid_upload = hl.HyperLinkCtrl( self.link_rapid_upload = hl.HyperLinkCtrl(
self.panel, self.panel,
wx.ID_ANY, wx.ID_ANY,
"Rapid Uploader", "Rapid",
URL=f"{self.base_site_url}/rapids/create/", URL=f"{self.base_site_url}/rapids/create/",
) )
# self.panel.sizer.Add(self.link_rapid_upload, 0, wx.ALL, 10) # self.panel.sizer.Add(self.link_rapid_upload, 0, wx.ALL, 10)
@@ -586,10 +589,17 @@ class AnonGui(wx.App):
"Long Series", "Long Series",
URL=f"{self.base_site_url}/longs/create/series", URL=f"{self.base_site_url}/longs/create/series",
) )
self.link_atlas_case = hl.HyperLinkCtrl(
self.panel,
wx.ID_ANY,
"Atlas Case",
URL=f"{self.base_site_url}/atlas/case/create/",
)
# self.panel.sizer.Add(self.link_long_upload, 0, wx.ALL, 10) # self.panel.sizer.Add(self.link_long_upload, 0, wx.ALL, 10)
hoz_links = wx.BoxSizer(wx.HORIZONTAL) hoz_links = wx.BoxSizer(wx.HORIZONTAL)
hoz_links.Add(self.link_rapid_upload, 1, wx.EXPAND) hoz_links.Add(self.link_rapid_upload, 1, wx.EXPAND)
hoz_links.Add(self.link_long_upload, 1, wx.EXPAND) hoz_links.Add(self.link_long_upload, 1, wx.EXPAND)
hoz_links.Add(self.link_atlas_case, 1, wx.EXPAND)
self.panel.sizer.Add(hoz_links, 1, wx.EXPAND) self.panel.sizer.Add(hoz_links, 1, wx.EXPAND)
# self.dirctrl = wx.GenericDirCtrl(self.panel, wx.ID_ANY, # self.dirctrl = wx.GenericDirCtrl(self.panel, wx.ID_ANY,
@@ -598,13 +608,18 @@ class AnonGui(wx.App):
# wx.DIRCTRL_3D_INTERNAL | # wx.DIRCTRL_3D_INTERNAL |
# wx.DIRCTRL_MULTIPLE, # wx.DIRCTRL_MULTIPLE,
# filter="Dicom files (*.dcm)|*.dcm") # filter="Dicom files (*.dcm)|*.dcm")
upload_drag_sizer = wx.BoxSizer(wx.HORIZONTAL)
self.drag_button = wx.Button( self.drag_button = wx.Button(
self.panel, id=wx.ID_ANY, label="Click here to drag files" self.panel, id=wx.ID_ANY, label="Drag"
) )
self.drag_button.SetToolTip("Click here to drag files")
self.upload_button = wx.Button( self.upload_button = wx.Button(
self.panel, id=wx.ID_ANY, label="Click here to upload files" self.panel, id=wx.ID_ANY, label="Click here to upload files"
) )
self.upload_button.Hide() self.upload_button.SetToolTip("Upload files to the server. You must be logged in.")
self.upload_button.Disable()
upload_drag_sizer.Add(self.upload_button, 4, wx.EXPAND)
upload_drag_sizer.Add(self.drag_button, 1, wx.EXPAND)
# Use some sizers to see layout options # Use some sizers to see layout options
# self.panel.sizer.Add(self.dirctrl, 1, wx.EXPAND) # self.panel.sizer.Add(self.dirctrl, 1, wx.EXPAND)
@@ -630,20 +645,25 @@ class AnonGui(wx.App):
self.list_ctrl.InsertColumn(6, "Hash") self.list_ctrl.InsertColumn(6, "Hash")
self.list_ctrl.InsertColumn(7, "Series Instance UID") self.list_ctrl.InsertColumn(7, "Series Instance UID")
# self.UpdateListCtrl() # self.UpdateListCtrl()
self.login_button = wx.Button(self.panel, id=wx.ID_ANY, label="Login") self.login_button = wx.Button(self.panel, id=wx.ID_ANY, label="Login")
self.login_button.SetForegroundColour(wx.BLUE) self.login_button.SetForegroundColour(wx.BLUE)
self.login_button.SetBackgroundColour(wx.WHITE)
self.login_button.SetToolTip("Click to login to the server")
self.clear_files_button = wx.Button( self.clear_files_button = wx.Button(
self.panel, id=wx.ID_ANY, label="Clear files" self.panel, id=wx.ID_ANY, label="Clear files"
) )
self.clear_files_button.SetToolTip("Click to clear all files.")
self.refresh_files_button = wx.Button(self.panel, id=wx.ID_ANY, label="Refresh") self.refresh_files_button = wx.Button(self.panel, id=wx.ID_ANY, label="Refresh")
self.reorder_files_button = wx.Button(self.panel, id=wx.ID_ANY, label="Reorder") self.reorder_files_button = wx.Button(self.panel, id=wx.ID_ANY, label="Reorder")
self.reorder_files_button.SetToolTip("Click to reorder files as they are shown below. This will sequentially rename the files. Please note this is usually better done once the files have been uploaded.")
self.reannonymise_files_button = wx.Button( self.reannonymise_files_button = wx.Button(
self.panel, id=wx.ID_ANY, label="Reannonymise" self.panel, id=wx.ID_ANY, label="Reannonymise"
) )
self.reannonymise_files_button.SetToolTip("Click to reannonymise the currently loaded files.")
self.manual_load_button = wx.Button(self.panel, id=wx.ID_ANY, label="Load") self.manual_load_button = wx.Button(self.panel, id=wx.ID_ANY, label="Load")
self.manual_load_button.SetToolTip("Click to manually load dicom from a directory.")
# wx.Bind(self.clear_files_button, ) # wx.Bind(self.clear_files_button, )
self.Bind(wx.EVT_BUTTON, self.Login, self.login_button) self.Bind(wx.EVT_BUTTON, self.Login, self.login_button)
@@ -651,11 +671,12 @@ class AnonGui(wx.App):
self.Bind(wx.EVT_BUTTON, lambda evt: self.LoadDir(), self.refresh_files_button) self.Bind(wx.EVT_BUTTON, lambda evt: self.LoadDir(), self.refresh_files_button)
self.Bind(wx.EVT_BUTTON, self.ReorderFiles, self.reorder_files_button) self.Bind(wx.EVT_BUTTON, self.ReorderFiles, self.reorder_files_button)
self.Bind(wx.EVT_BUTTON, self.ReAnnonymiseFiles, self.reannonymise_files_button) self.Bind(wx.EVT_BUTTON, self.ReAnnonymiseFiles, self.reannonymise_files_button)
self.Bind( #self.Bind(
wx.EVT_BUTTON, # wx.EVT_BUTTON,
lambda evt: self.AnnonymiseFilesInDir(self.input_dir, self.dir), # lambda evt: self.AnnonymiseFilesInDir(self.input_dir, self.dir),
self.manual_load_button, # self.manual_load_button,
) #)
self.Bind(wx.EVT_BUTTON, self.import_from_dir, self.manual_load_button)
# Use some sizers to see layout options # Use some sizers to see layout options
# self.panel.sizer.Add(self.dirctrl, 1, wx.EXPAND) # self.panel.sizer.Add(self.dirctrl, 1, wx.EXPAND)
@@ -672,13 +693,16 @@ class AnonGui(wx.App):
self.panel.sizer.Add(self.series_grid, 2, wx.EXPAND) self.panel.sizer.Add(self.series_grid, 2, wx.EXPAND)
self.panel.sizer.Add(self.list_ctrl, 8, wx.EXPAND) self.panel.sizer.Add(self.list_ctrl, 8, wx.EXPAND)
self.panel.sizer.Add(self.drag_button, 2, wx.EXPAND) #self.panel.sizer.Add(self.drag_button, 2, wx.EXPAND)
self.panel.sizer.Add(self.upload_button, 2, wx.EXPAND) #self.panel.sizer.Add(self.upload_button, 2, wx.EXPAND)
self.panel.sizer.Add(upload_drag_sizer, 2, wx.EXPAND)
self.progress_sizer = wx.BoxSizer(wx.VERTICAL) self.progress_sizer = wx.BoxSizer(wx.VERTICAL)
self.progress_bar = wx.Gauge(self.panel, style=wx.GA_HORIZONTAL|wx.GA_PROGRESS) self.progress_bar = wx.Gauge(
#self.progress_bar = PG.PyGauge(self.panel, style=wx.GA_HORIZONTAL|wx.GA_PROGRESS) self.panel, style=wx.GA_HORIZONTAL | wx.GA_PROGRESS
#self.progress_bar.SetDrawValue(draw=True, drawPercent=True, font=None, colour=wx.RED, formatString=None) )
# self.progress_bar = PG.PyGauge(self.panel, style=wx.GA_HORIZONTAL|wx.GA_PROGRESS)
# self.progress_bar.SetDrawValue(draw=True, drawPercent=True, font=None, colour=wx.RED, formatString=None)
self.progress_text = wx.StaticText(self.panel, label="Text") self.progress_text = wx.StaticText(self.panel, label="Text")
self.progress_sizer.Add(self.progress_bar, 2, wx.EXPAND) self.progress_sizer.Add(self.progress_bar, 2, wx.EXPAND)
self.progress_sizer.Add(self.progress_text, 2, wx.EXPAND) self.progress_sizer.Add(self.progress_text, 2, wx.EXPAND)
@@ -691,18 +715,21 @@ class AnonGui(wx.App):
self.panel.sizer.Fit(self.panel) self.panel.sizer.Fit(self.panel)
self.frame.Show() self.frame.Show()
# self.spinner.Hide() # self.spinner.Hide()
wx.CallAfter(self.post_init)
return super().OnInit()
def post_init(self):
self.AnnonymiseFilesInDir(self.input_dir, self.dir) self.AnnonymiseFilesInDir(self.input_dir, self.dir)
self.Bind(wx.EVT_KEY_DOWN, self.onKeyPress) self.Bind(wx.EVT_KEY_DOWN, self.onKeyPress)
self.image_hash_check_in_progress = False self.image_hash_check_in_progress = False
self.duplicate_check_timer = wx.Timer() self.duplicate_check_timer = wx.Timer()
self.Bind(wx.EVT_TIMER, self.check_image_hashes, self.duplicate_check_timer) self.Bind(wx.EVT_TIMER, self.check_image_hashes, self.duplicate_check_timer)
self.duplicate_check_timer.Start(2000) self.duplicate_check_timer.Start(2000)
return super().OnInit()
def populate_series_grid(self): def populate_series_grid(self):
self.series_grid.series = [] self.series_grid.series = []
@@ -717,6 +744,15 @@ class AnonGui(wx.App):
self.series_grid.display_series() self.series_grid.display_series()
def import_from_dir(self, event):
default_path = str(self.input_dir.resolve())
with wx.DirDialog(
self.frame, "Choose a directory", style=wx.DD_DEFAULT_STYLE, defaultPath=default_path
) as dlg:
if dlg.ShowModal() == wx.ID_OK:
load_path = Path(dlg.GetPath())
self.AnnonymiseFilesInDir(load_path, self.dir)
def AnnonymiseFilesInDir(self, input_dir, output_dir): def AnnonymiseFilesInDir(self, input_dir, output_dir):
logger.debug("AnnonymiseFilesInDir") logger.debug("AnnonymiseFilesInDir")
logger.debug(f"input: {input_dir} / output {output_dir}") logger.debug(f"input: {input_dir} / output {output_dir}")
@@ -726,21 +762,26 @@ class AnonGui(wx.App):
else: else:
return return
if not files:
logger.debug("No files to annonymise")
wx.adv.NotificationMessage("Annonymise files", "No files to annonymise").Show()
return
logger.debug(files) logger.debug(files)
#files = order_files_by_dicom_attribute(files) # files = order_files_by_dicom_attribute(files)
#progress_dialog = wx.ProgressDialog( # progress_dialog = wx.ProgressDialog(
# "Annonymise files", # "Annonymise files",
# "Removing data...", # "Removing data...",
# maximum=len(files), # maximum=len(files),
# style=wx.PD_APP_MODAL | wx.PD_ELAPSED_TIME | wx.PD_ESTIMATED_TIME, # style=wx.PD_APP_MODAL | wx.PD_ELAPSED_TIME | wx.PD_ESTIMATED_TIME,
#) # )
with self.progress(len(files), "Annonymise files") as p: with self.progress(len(files), "Annonymise files") as p:
#p.SetRange(len(files)) # p.SetRange(len(files))
for n, file in enumerate(files): for n, file in enumerate(files):
#progress_dialog.Update(n) # progress_dialog.Update(n)
p.update(n) p.update(n)
new_filepath: Path new_filepath: Path
# Get next available filename # Get next available filename
@@ -751,36 +792,39 @@ class AnonGui(wx.App):
i += 1 i += 1
# new_filepath = Path(output_dir).joinpath(f"IMG_{i:03}.dcm") # new_filepath = Path(output_dir).joinpath(f"IMG_{i:03}.dcm")
dataset, filepath = anonymize_file(file, new_filepath) dataset, filepath = anonymize_file(file, new_filepath, remove_original=self.remove_files_on_annonymisation)
self.add_datails_to_file_detail_map(dataset, filepath) self.add_datails_to_file_detail_map(dataset, filepath)
#progress_dialog.Destroy() # progress_dialog.Destroy()
self.LoadDir(self.dir) self.LoadDir(self.dir)
@contextlib.contextmanager @contextlib.contextmanager
def progress(self, total: int, text: str="Working"): def progress(self, total: int, text: str = "Working"):
#self.progress_sizer.Show() # self.progress_sizer.Show()
self.progress_text.SetLabelText(text) self.progress_text.SetLabelText(text)
self.progress_bar.SetRange(total) self.progress_bar.SetRange(total)
self.progress_sizer.ShowItems(show=True) self.progress_sizer.ShowItems(show=True)
self.panel.Layout() self.panel.Layout()
#self.panel.sizer.Fit(self.panel) self.panel.sizer.Fit(self.panel)
try: try:
class P():
class P:
def __init__(self, gui, total, text): def __init__(self, gui, total, text):
self.gui = gui self.gui = gui
self.text = text self.text = text
self.total = total self.total = total
def update(self, n: int): def update(self, n: int):
self.gui.progress_bar.SetValue(n) self.gui.progress_bar.SetValue(n)
self.gui.progress_text.SetLabelText(f"{self.text} : {n}") self.gui.progress_text.SetLabelText(f"{self.text} : {n}")
yield P(self, total, text) yield P(self, total, text)
finally: finally:
#self.progress_sizer.Hide() # self.progress_sizer.Hide()
self.progress_sizer.ShowItems(show=False) self.progress_sizer.ShowItems(show=False)
self.panel.Layout() self.panel.Layout()
#self.panel.SetAutoLayout(1) # self.panel.SetAutoLayout(1)
#self.panel.sizer.Fit(self.panel) # self.panel.sizer.Fit(self.panel)
def onKeyPress(self, event): def onKeyPress(self, event):
keycode = event.GetKeyCode() keycode = event.GetKeyCode()
@@ -822,6 +866,7 @@ class AnonGui(wx.App):
return super().OnExit() return super().OnExit()
def LoadDir(self, dir=None, refresh=True, clear_file_detail_map=False): def LoadDir(self, dir=None, refresh=True, clear_file_detail_map=False):
"""Loads data from the output directory (annonymised files)"""
if clear_file_detail_map: if clear_file_detail_map:
self.file_detail_map = {} self.file_detail_map = {}
self.file_duplicate_check = {} self.file_duplicate_check = {}
@@ -871,12 +916,20 @@ class AnonGui(wx.App):
for i in range(self.list_ctrl.GetItemCount()): for i in range(self.list_ctrl.GetItemCount()):
if self.list_ctrl.IsSelected(i): if self.list_ctrl.IsSelected(i):
path = self.list_ctrl.GetItemPyData(i)["file"] path = self.list_ctrl.GetItemPyData(i)["file"]
if path in self.file_duplicate_check and self.file_duplicate_check[path]["id"]: if (
path in self.file_duplicate_check
and self.file_duplicate_check[path]["id"]
):
menu.Append(3, "View on site") menu.Append(3, "View on site")
menu.Bind(wx.EVT_MENU, lambda evt: webbrowser.open(f"{self.base_site_url}{self.file_duplicate_check[path]['url']}"), id=3) menu.Bind(
wx.EVT_MENU,
lambda evt: webbrowser.open(
f"{self.base_site_url}{self.file_duplicate_check[path]['url']}"
),
id=3,
)
break break
self.frame.PopupMenu(menu) self.frame.PopupMenu(menu)
def ViewDicom(self, event): def ViewDicom(self, event):
@@ -900,13 +953,15 @@ class AnonGui(wx.App):
tempdir = Path(tempfile.gettempdir()) tempdir = Path(tempfile.gettempdir())
to_move = [] to_move = []
for i in range(self.list_ctrl.GetItemCount()): with self.progress(self.list_ctrl.GetItemCount(), "Reannonymise files") as p:
path = self.list_ctrl.GetItemPyData(i)["file"] for i in range(self.list_ctrl.GetItemCount()):
logger.debug("--", path) p.update(i)
# paths.append(path) path = self.list_ctrl.GetItemPyData(i)["file"]
new_path = annonymise(path, tempdir, run_gui=False) logger.debug("--", path)
os.remove(path) # paths.append(path)
to_move.append((new_path, Path(self.dir, new_path.name))) new_path = annonymise(path, tempdir, run_gui=False)
os.remove(path)
to_move.append((new_path, Path(self.dir, new_path.name)))
for path, new_path in to_move: for path, new_path in to_move:
logger.debug("**", path, new_path) logger.debug("**", path, new_path)
@@ -956,11 +1011,11 @@ class AnonGui(wx.App):
dlg.ShowModal() dlg.ShowModal()
def ClearFiles(self, event=None, load_dir: bool=True): def ClearFiles(self, event=None, load_dir: bool = True):
files = Path(self.dir).glob("*") files = Path(self.dir).glob("*")
for f in files: for f in files:
os.remove(f) os.remove(f)
if load_dir: if load_dir:
self.LoadDir(clear_file_detail_map=True) self.LoadDir(clear_file_detail_map=True)
@@ -985,7 +1040,6 @@ class AnonGui(wx.App):
slice_location = str(dataset.SliceLocation) slice_location = str(dataset.SliceLocation)
except: except:
slice_location = "..." slice_location = "..."
series_instances_uid = str(dataset.SeriesInstanceUID) series_instances_uid = str(dataset.SeriesInstanceUID)
d2 = { d2 = {
@@ -995,36 +1049,36 @@ class AnonGui(wx.App):
"name": patient_name, "name": patient_name,
} }
#md5 = hashlib.md5() # md5 = hashlib.md5()
#first = True # first = True
#for i in dataset.pixel_array.astype(str).flatten(): # for i in dataset.pixel_array.astype(str).flatten():
# if first: # if first:
# first = False # first = False
# md5.update(f"{i}".encode()) # md5.update(f"{i}".encode())
# else: # else:
# md5.update(f",{i}".encode()) # md5.update(f",{i}".encode())
#md5.update(dataset.PixelData) # md5.update(dataset.PixelData)
#md5.update("".join(dataset.pixel_array.astype(str).flatten()).encode()) # md5.update("".join(dataset.pixel_array.astype(str).flatten()).encode())
#md5.update(np.char.join("", dataset.pixel_array.astype(str).flatten()).encode()) # md5.update(np.char.join("", dataset.pixel_array.astype(str).flatten()).encode())
#hash = md5.hexdigest() # hash = md5.hexdigest()
#print(hash) # print(hash)
#md5 = hashlib.md5() # md5 = hashlib.md5()
##hash = md5.hexdigest() ##hash = md5.hexdigest()
##md5 = hashlib.md5() ##md5 = hashlib.md5()
##first = True ##first = True
##s = ",".join([f"{i}" for i in dataset.pixel_array.astype(str).flatten()]).encode() ##s = ",".join([f"{i}" for i in dataset.pixel_array.astype(str).flatten()]).encode()
##print(s) ##print(s)
#print(dataset.PixelData[:20]) # print(dataset.PixelData[:20])
#print(len(dataset.PixelData)) # print(len(dataset.PixelData))
#md5.update(dataset.PixelData) # md5.update(dataset.PixelData)
#hash = md5.hexdigest() # hash = md5.hexdigest()
hasher = blake3() hasher = blake3()
hasher.update(dataset.PixelData) hasher.update(dataset.PixelData)
hash = hasher.hexdigest() hash = hasher.hexdigest()
#dataset.PixelData # dataset.PixelData
d = ( d = (
file.name, file.name,
@@ -1034,23 +1088,23 @@ class AnonGui(wx.App):
series_desc, series_desc,
slice_location, slice_location,
hash, hash,
series_instances_uid series_instances_uid,
) )
#hasher = blake3() # hasher = blake3()
#first = True # first = True
#for i in dataset.pixel_array.astype(str).flatten(): # for i in dataset.pixel_array.astype(str).flatten():
# if first: # if first:
# first = False # first = False
# hasher.update(f"{i}".encode()) # hasher.update(f"{i}".encode())
# else: # else:
# hasher.update(f",{i}".encode()) # hasher.update(f",{i}".encode())
#hash = hasher.digest() # hash = hasher.digest()
#hash = get_file_hash(file, hasher="md5") # hash = get_file_hash(file, hasher="md5")
#hash = None # If we don't use the hash... # hash = None # If we don't use the hash...
self.file_detail_map[file] = d, hash, d2 self.file_detail_map[file] = d, hash, d2
return d, hash, d2 return d, hash, d2
@@ -1061,14 +1115,14 @@ class AnonGui(wx.App):
n = 0 n = 0
DATA = {} DATA = {}
#progress_dialog = wx.ProgressDialog( # progress_dialog = wx.ProgressDialog(
# "Loading files", # "Loading files",
# "Extracting data from files", # "Extracting data from files",
# maximum=len(self.files), # maximum=len(self.files),
# style=wx.PD_APP_MODAL | wx.PD_ELAPSED_TIME | wx.PD_ESTIMATED_TIME, # style=wx.PD_APP_MODAL | wx.PD_ELAPSED_TIME | wx.PD_ESTIMATED_TIME,
#) # )
with self.progress((len(self.files)), "Loading files") as p: with self.progress((len(self.files)), "Loading files") as p:
#p.SetRange(len(self.files)) # p.SetRange(len(self.files))
self.series_map = defaultdict(list) self.series_map = defaultdict(list)
self.series_map_details = defaultdict(dict) self.series_map_details = defaultdict(dict)
@@ -1076,7 +1130,7 @@ class AnonGui(wx.App):
hashes = [] hashes = []
for n, f in enumerate(self.files): for n, f in enumerate(self.files):
#progress_dialog.Update(n) # progress_dialog.Update(n)
p.update(n) p.update(n)
# dataset = pydicom.read_file(f) # dataset = pydicom.read_file(f)
@@ -1094,16 +1148,15 @@ class AnonGui(wx.App):
hashes.append(hash) hashes.append(hash)
series_instances_uid = d2["series_instances_uid"] series_instances_uid = d2["series_instances_uid"]
try: try:
self.series_map[series_instances_uid].append(f) self.series_map[series_instances_uid].append(f)
self.series_map_details[series_instances_uid][ self.series_map_details[series_instances_uid][
"series_description" "series_description"
] = d2["series_description"] ] = d2["series_description"]
self.series_map_details[series_instances_uid]["study_description"] = d2[ self.series_map_details[series_instances_uid][
"study_description" "study_description"
] ] = d2["study_description"]
self.series_map_details[series_instances_uid]["name"] = d2["name"] self.series_map_details[series_instances_uid]["name"] = d2["name"]
except: except:
logger.debug(f"Unable to get Series Instance UID: {f.name}") logger.debug(f"Unable to get Series Instance UID: {f.name}")
@@ -1122,10 +1175,9 @@ class AnonGui(wx.App):
self.list_ctrl.UpdateData(DATA) self.list_ctrl.UpdateData(DATA)
self.populate_series_grid() self.populate_series_grid()
# progress_dialog.Destroy()
#progress_dialog.Destroy() # if hashes:
#if hashes:
# self.check_image_hashes(hashes) # self.check_image_hashes(hashes)
def check_image_hashes(self, evt): def check_image_hashes(self, evt):
@@ -1133,15 +1185,12 @@ class AnonGui(wx.App):
self.image_hash_check_in_progress = True self.image_hash_check_in_progress = True
to_check = self.file_detail_map.keys() - self.file_duplicate_check.keys() to_check = self.file_detail_map.keys() - self.file_duplicate_check.keys()
print(to_check)
if to_check: if to_check:
hash_file_map = {} hash_file_map = {}
for file in to_check: for file in to_check:
hash_file_map[self.file_detail_map[file][1]] = file hash_file_map[self.file_detail_map[file][1]] = file
hashes = list(hash_file_map.keys()) hashes = list(hash_file_map.keys())
self.rqst.headers["X-CSRFToken"] = self.rqst.cookies["csrftoken"] self.rqst.headers["X-CSRFToken"] = self.rqst.cookies["csrftoken"]
@@ -1150,7 +1199,7 @@ class AnonGui(wx.App):
resp = self.rqst.post( resp = self.rqst.post(
f"{self.base_site_url}/api/atlas/check_image_hashes/", f"{self.base_site_url}/api/atlas/check_image_hashes/",
data=json.dumps(hashes), data=json.dumps(hashes),
#files=files, # files=files,
) )
for hash, dup in resp.json().items(): for hash, dup in resp.json().items():
@@ -1180,14 +1229,14 @@ class AnonGui(wx.App):
files_to_upload[i : i + n] for i in range(0, len(files_to_upload), n) files_to_upload[i : i + n] for i in range(0, len(files_to_upload), n)
] ]
#progress_dialog = wx.ProgressDialog( # progress_dialog = wx.ProgressDialog(
# "Uploading files", # "Uploading files",
# "Uploading files. This is done in batches...", # "Uploading files. This is done in batches...",
# maximum=len(chunked_files), # maximum=len(chunked_files),
# style=wx.PD_ELAPSED_TIME | wx.PD_ESTIMATED_TIME, # style=wx.PD_ELAPSED_TIME | wx.PD_ESTIMATED_TIME,
#) # )
with self.progress(len(chunked_files), "Uploading files (in batches)") as p: with self.progress(len(chunked_files), "Uploading files (in batches)") as p:
#p.SetRange(len(chunked_files)) # p.SetRange(len(chunked_files))
upload_file_list = [] upload_file_list = []
duplicate_file_list = [] duplicate_file_list = []
@@ -1209,7 +1258,7 @@ class AnonGui(wx.App):
return resp return resp
p.update(n) p.update(n)
#progress_dialog.Update(n, f"Uploading batch {n}/{len(chunked_files)}") # progress_dialog.Update(n, f"Uploading batch {n}/{len(chunked_files)}")
logger.debug(f"n: {n}") logger.debug(f"n: {n}")
# try to upload the files # try to upload the files
@@ -1228,11 +1277,13 @@ class AnonGui(wx.App):
duplicate_file_list.extend(resp.json()["duplicates"]) duplicate_file_list.extend(resp.json()["duplicates"])
continue continue
#progress_dialog.Destroy() # progress_dialog.Destroy()
print(upload_file_list) print(upload_file_list)
print(duplicate_file_list) print(duplicate_file_list)
wx.CallAfter( wx.CallAfter(
self.upload_complete_message, upload_file_list, duplicate_file_list self.upload_complete_message, upload_file_list, duplicate_file_list
) )
@@ -1263,26 +1314,41 @@ class AnonGui(wx.App):
def runGUI( def runGUI(
ctx: typer.Context, ctx: typer.Context,
input_dir: Path = "C:\\Temp\\", input_dir: Path = "C:\\Temp\\",
#input_dir: Path = "/home/ross/temp/in/",
output_dir: Path = "C:\\temp_upload\\", output_dir: Path = "C:\\temp_upload\\",
#output_dir: Path = "/home/ross/temp/out/",
silent_fail: bool = False, silent_fail: bool = False,
clear_files: bool = True, clear_files: bool = True,
clear_files_on_close: bool = True, clear_files_on_close: bool = True,
remove_files_on_annonymisation: bool = True,
dev: bool = False, dev: bool = False,
): ):
if "linux" in sys.platform:
input_dir = Path("/home/ross/temp/in/")
output_dir = Path("/home/ross/temp/out/")
if ctx.invoked_subcommand is None: if ctx.invoked_subcommand is None:
try: try:
typer.echo("run gui") typer.echo("run gui")
except AttributeError: # No console except AttributeError: # No console
pass pass
launchGUI( launchGUI(
input_dir, output_dir, silent_fail, clear_files, clear_files_on_close, dev input_dir,
output_dir,
silent_fail,
clear_files,
clear_files_on_close,
dev,
remove_files_on_annonymisation,
) )
def launchGUI( def launchGUI(
input_dir, output_dir, silent_fail, clear_files, clear_files_on_close, dev input_dir,
output_dir,
silent_fail,
clear_files,
clear_files_on_close,
dev,
remove_files_on_annonymisation,
): ):
app = AnonGui( app = AnonGui(
input_dir=input_dir, input_dir=input_dir,
@@ -1291,6 +1357,7 @@ def launchGUI(
clear_files=clear_files, clear_files=clear_files,
clear_files_on_close=clear_files_on_close, clear_files_on_close=clear_files_on_close,
dev=dev, dev=dev,
remove_files_on_annonymisation=remove_files_on_annonymisation,
) )
app.MainLoop() app.MainLoop()