From dc4ec36ca70e6b44864463825580f954c3c0404f Mon Sep 17 00:00:00 2001
From: Timothe Jost <timothe.jost@wanadoo.fr>
Date: Sat, 16 Mar 2024 04:31:05 +0100
Subject: [PATCH] format and set preprocessing files to "adaptation" instead of
preproc_data
---
app.py | 100 ++++++++++++++++++---------------------------------------
1 file changed, 32 insertions(+), 68 deletions(-)
diff --git a/app.py b/app.py
index 6c20d4e..217c58a 100644
--- a/app.py
+++ b/app.py
@@ -44,9 +44,7 @@ pages = {
app.layout = html.Div(
[
- html.Div(
- className="ribbon", id="ribbon_container", style={"margin-bottom": 75}
- ),
+ html.Div(className="ribbon", id="ribbon_container", style={"margin-bottom": 75}),
html.Div(
children=[
dcc.Location(id="url", refresh=False),
@@ -69,22 +67,18 @@ def create_menu(session_uuid, session_alias):
dropdown = []
else:
alyx_label = "Open in Alyx"
- alyx_adress = (
- f"http://haiss-alyx.local/admin/actions/session/{session_uuid}/change/"
- )
+ alyx_adress = f"http://haiss-alyx.local/admin/actions/session/{session_uuid}/change/"
dropdown = [
html.Div(
[
f"Session {session_alias}",
html.Div(
- [
- html.A(name, href=link.format(session_uuid=session_uuid))
- for name, link in pages.items()
- ],
+ [html.A(name, href=link.format(session_uuid=session_uuid)) for name, link in pages.items()],
className="dropdown-content",
),
],
- className="dropdown-link-menu", id = "session-name-title",
+ className="dropdown-link-menu",
+ id="session-name-title",
)
]
print("Session id is : ", session_uuid, "alias is : ", session_alias)
@@ -152,28 +146,15 @@ def dash_container_router(pathname):
return dash.no_update
for route, route_item in func_routes.items():
if route_item["route_pattern"].match(pathname):
- print(
- pathname
- + " match : "
- + route
- + "with pattern : "
- + route_item["route_pattern"].pattern
- )
+ print(pathname + " match : " + route + "with pattern : " + route_item["route_pattern"].pattern)
kwargs = {}
kwags_matches = route_item["route_pattern"].findall(pathname)
if kwags_matches:
if len(route_item["kwargs_names"]) > 1:
kwags_matches = kwags_matches[0]
- kwargs = {
- name: match
- for name, match in zip(route_item["kwargs_names"], kwags_matches)
- }
- return route_item["func"](
- **kwargs
- ) # call the appropriate routed function here, with **kwargs
- return html.Div(
- "404 Not Found: The resource could not be found.", className="error_message"
- )
+ kwargs = {name: match for name, match in zip(route_item["kwargs_names"], kwags_matches)}
+ return route_item["func"](**kwargs) # call the appropriate routed function here, with **kwargs
+ return html.Div("404 Not Found: The resource could not be found.", className="error_message")
def perform_data_registration(uuid, dry_run=True):
@@ -182,12 +163,8 @@ def perform_data_registration(uuid, dry_run=True):
selected_session_folder = session_details["path"]
selected_session_folder = convert_mount(selected_session_folder)
- results = auto_rename_session_files_to_alf(
- selected_session_folder, dry_run=dry_run, return_tables=True
- )
- results["names_after_renaming"] = [
- convert_mount(path, reverse=True) for path in results["names_after_renaming"]
- ]
+ results = auto_rename_session_files_to_alf(selected_session_folder, dry_run=dry_run, return_tables=True)
+ results["names_after_renaming"] = [convert_mount(path, reverse=True) for path in results["names_after_renaming"]]
try:
register_files(results["names_after_renaming"], uuid, dry_run=dry_run)
except:
@@ -197,14 +174,12 @@ def perform_data_registration(uuid, dry_run=True):
@dash_route("/dashboard/data-registration/<uuid>/check", strict_slashes=False)
def display_data_registration_check(uuid):
- with temporary_logger('stdout') as logger:
+ with temporary_logger("stdout") as logger:
tables = perform_data_registration(uuid, dry_run=True)
log = logger.getvalue()
- log_text = html.Pre(log, style={'whiteSpace': 'pre-wrap', 'wordBreak': 'break-all'})
+ log_text = html.Pre(log, style={"whiteSpace": "pre-wrap", "wordBreak": "break-all"})
conflict_table = display_table(tables["conflicts_df"], "Conflicts Table")
- comparison_table = display_table(
- tables["comparison_df"], "File Renaming Comparisons Table"
- )
+ comparison_table = display_table(tables["comparison_df"], "File Renaming Comparisons Table")
redirect_button = html.Div(
dcc.Link(
@@ -228,6 +203,7 @@ def display_data_registration_check(uuid):
]
)
+
def display_table(df, title=None):
def drop_multiliners(cell):
try:
@@ -261,12 +237,12 @@ def display_table(df, title=None):
if title is None:
title = ""
- style_header = {'font-family': 'Roboto, sans-serif', 'font-weight': 'bold', 'font-size': '16px'}
- style_table= {"width": "100vw", "overflow-x": "auto"}
- style_cell = {'font-family': 'Roboto, sans-serif', 'font-size': '14px','text-align': 'center'}
+ style_header = {"font-family": "Roboto, sans-serif", "font-weight": "bold", "font-size": "16px"}
+ style_table = {"width": "100vw", "overflow-x": "auto"}
+ style_cell = {"font-family": "Roboto, sans-serif", "font-size": "14px", "text-align": "center"}
if len(df):
- style_cell.update({'width': '{}%'.format(100/len(df.columns))})
-
+ style_cell.update({"width": "{}%".format(100 / len(df.columns))})
+
return html.Div(
[
html.Div(title, className="table_title"),
@@ -280,8 +256,8 @@ def display_table(df, title=None):
page_size=25,
style_header=style_header,
style_table=style_table,
- style_cell = style_cell,
- id = "pandas_table"
+ style_cell=style_cell,
+ id="pandas_table",
),
]
)
@@ -392,14 +368,12 @@ def get_trials_df(uuid):
"404 Not Found: The supplied session doesn't exist",
className="error_message",
)
- session = connector.to_session_details(
- connector.alyx.rest("sessions", "read", id=uuid)
- )
+ session = connector.to_session_details(connector.alyx.rest("sessions", "read", id=uuid))
df_path = os.path.join(
convert_mount(session.path),
"preprocessing_saves",
- "preproc_data.trials_df.pickle",
+ "adaptation.trials_df.pickle",
)
df = pd.read_pickle(df_path)
df.loc[:, "trial_nb"] = df.index
@@ -413,7 +387,7 @@ def display_trials_df_table(uuid):
return display_table(get_trials_df(uuid), "Trials Table")
except FileNotFoundError:
return html.Div(
- "404 Not Found: preproc_data.trials_df was not found for this session",
+ "404 Not Found: adaptation.trials_df was not found for this session",
className="error_message",
)
@@ -424,7 +398,7 @@ def display_trials_df_plot(uuid):
return display_2d_plot(get_trials_df(uuid))
except FileNotFoundError:
return html.Div(
- "404 Not Found: preproc_data.trials_df was not found for this session",
+ "404 Not Found: adaptation.trials_df was not found for this session",
className="error_message",
)
@@ -451,7 +425,7 @@ def display_data_management_plot(uuid):
@dash_route("/dashboard/")
def dashboard_home():
- return dcc.Location(pathname='/', id='url_redirecting', refresh=True)
+ return dcc.Location(pathname="/", id="url_redirecting", refresh=True)
@server.route("/images/<uuid_key>", strict_slashes=False)
@@ -461,7 +435,7 @@ def serve_images(uuid_key):
return render_template(
"images_gallery.html",
image_groups=images,
- dropdown_links = {key : link.format(session_uuid=uuid_key) for key, link in pages.items()},
+ dropdown_links={key: link.format(session_uuid=uuid_key) for key, link in pages.items()},
session_alias=session_object.alias,
session_uuid=uuid_key,
)
@@ -470,28 +444,21 @@ def serve_images(uuid_key):
uuid_key = connector.to_eid(uuid_key) # uuid key is provided by the page url
if uuid_key is None:
return "Error: Invalid UUID key provided", 400
- session_object = connector.to_session_details(
- connector.alyx.rest("sessions", "read", id=uuid_key, no_cache=True)
- )
+ session_object = connector.to_session_details(connector.alyx.rest("sessions", "read", id=uuid_key, no_cache=True))
folder_path = os.path.join(session_object.path, "figures")
try:
folder_path = convert_mount(folder_path)
except IOError:
return render()
try:
- image_files = [
- file for file in os.listdir(folder_path) if file.endswith((".png", ".jpg"))
- ]
+ image_files = [file for file in os.listdir(folder_path) if file.endswith((".png", ".jpg"))]
except (
FileNotFoundError
) as e: # FileNotFoundError if toplevel figures listed folder does not exist for this session.
return render()
image_files.sort()
- image_groups = [
- natsorted(list(group))
- for _, group in groupby(image_files, lambda x: x.split(".")[1])
- ]
+ image_groups = [natsorted(list(group)) for _, group in groupby(image_files, lambda x: x.split(".")[1])]
images = [
[
{
@@ -537,10 +504,7 @@ def convert_mount(path, reverse=False):
@server.route("/image-directory/<path:path>")
def send_image(path):
folder, filename = os.path.split(path)
- if (
- not (folder[0] == "/" or folder[0] == "\\")
- and "ubuntu" in platform.version().lower()
- ):
+ if not (folder[0] == "/" or folder[0] == "\\") and "ubuntu" in platform.version().lower():
folder = (
"/" + folder
) # we make sure to have / in front of folder path to make sure the path is absolut, if we run on ubuntu
--
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