Skip to content

Commit

Permalink
Merge branch 'main1' into main_upstream
Browse files Browse the repository at this point in the history 
# Conflicts:
#	OMERO_metrics/dash_apps/dash_image_psf_beads.py
#	OMERO_metrics/tools/data_preperation.py
  • Loading branch information
@Wapaa
Wapaa committed Oct 4, 2024
2 parents a5f9ba9 + 152a796 commit 15ae803
Show file tree
Hide file tree
Showing 40 changed files with 4,459 additions and 1,407 deletions.
14 changes: 0 additions & 14 deletions OMERO_metrics/OMERO_metrics_settings.py
View file

This file was deleted.

438 changes: 438 additions & 0 deletions OMERO_metrics/dash_apps/dash_dataset_form.py
View file

Large diffs are not rendered by default.

102 changes: 37 additions & 65 deletions OMERO_metrics/dash_apps/dash_dataset_metrics.py
View file
Original file line number Diff line number Diff line change
@@ -1,13 +1,10 @@
import dash
import pandas as pd
from dash import dcc, html, dash_table
from dash import dcc, html
from django_plotly_dash import DjangoDash
import plotly.express as px
import dash_mantine_components as dmc
from dash_iconify import DashIconify

from datetime import datetime
import plotly.graph_objects as go
from skimage.exposure import rescale_intensity

external_scripts = [
Expand Down Expand Up @@ -38,27 +35,28 @@
[
dmc.Center(
[
dmc.Text(
id="title",
c=primary_color,
style={"fontSize": 30},
),
dmc.Group(
[
html.Img(
src="./assets/images/logo.png",
style={"width": "100px"},
),
dmc.Text(
"OMERO Metrics Dashboard",
c=primary_color,
style={"fontSize": 15},
dmc.Title(
"Field Of Illumination Dashboard",
c="#189A35",
size="h3",
mb=10,
mt=5,
),
]
),
]
],
style={
"background-color": "white",
"border-radius": "0.5rem",
"padding": "10px",
},
),
dmc.Divider(variant="solid"),
dmc.Grid(
id="group_image",
justify="space-between",
Expand All @@ -75,8 +73,9 @@
dmc.Select(
id="channel_dropdown_foi",
label="Select Channel",
clearable=False,
w="300",
value="channel 0",
value="0",
leftSection=DashIconify(
icon="radix-icons:magnifying-glass"
),
Expand All @@ -93,7 +92,7 @@
},
),
],
span="auto",
span="6",
),
dmc.GridCol(
[
Expand All @@ -110,14 +109,23 @@
)
]
),
dmc.Table(
id="km_table",
striped=True,
highlightOnHover=True,
className="table table-striped table-bordered",
dmc.ScrollArea(
[
dmc.Table(
id="km_table",
striped=True,
highlightOnHover=True,
className="table table-striped table-bordered",
styles={
"background-color": "white",
"width": "auto",
"height": "auto",
},
)
]
),
],
span="auto",
span="6",
),
],
),
Expand Down Expand Up @@ -199,10 +207,10 @@ def update_dropdow_menu(*args, **kwargs):
channel = kwargs["session_state"]["context"]["channel_names"]

channel_list = [
{"label": c.name, "value": f"channel {i}"}
for i, c in enumerate(channel.channels)
{"label": channel_name, "value": f"{i}"}
for i, channel_name in enumerate(channel)
]
data = [{"group": "Channels", "items": channel_list}]
data = channel_list
return data


Expand Down Expand Up @@ -241,8 +249,9 @@ def dataset_callback_intensity_map(*args, **kwargs):
df_intensity_profiles = kwargs["session_state"]["context"][
"intensity_profiles"
]
channel = int(args[0][-1])
image_channel = images[0, 0, :, :, channel]
channel = int(args[0])
image = images[channel]
image_channel = image[0, 0, :, :]
image_channel = rescale_intensity(
image_channel, in_range=(0, image_channel.max()), out_range=(0.0, 1.0)
)
Expand Down Expand Up @@ -288,40 +297,3 @@ def restyle_dataframe(df: pd.DataFrame, col: str) -> pd.DataFrame:
df, col, value
) # TODO: replace setattr with df.loc[:, col] = value
return df


# dmc.GridCol([dmc.Center([dmc.Text("Key Measurements", size="md")]),
# table2, dmc.Center([dmc.Text("Key Measurements for Field of Illumination", c="dimmed",
# size="sm")])]

#
# table2 = dash_table.DataTable(
# data=table_kkm.to_dict('records'),
# columns=[{"name": i, "id": i} for i in table_kkm.columns],
# style_table={"overflowX": "auto",
# "padding": "10px",
# "background": "white",
# "border": "thin, white, solid",
#
# },
# page_size=10,
# editable=False,
# style_cell={
# "textAlign": "center",
# "fontSize": 10,
# "font-family": "Roboto",
# "border": "thin, white, solid",
# "border-bottom": 'thin #dee2e6 solid'
#
# },
# style_header={
# "fontWeight": "bold",
# "font-family": "Roboto",
#
# "fontSize": 12,
# "textAlign": "center",
# "border": "thin, white, solid",
# "border-bottom": 'thin #dee2e6 solid'
# },
#
# )
88 changes: 48 additions & 40 deletions OMERO_metrics/dash_apps/dash_dataset_psf_beads.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -48,67 +48,75 @@
[
dmc.Center(
[
dmc.Text(
id="title",
c=primary_color,
style={"fontSize": 30},
),
dmc.Group(
[
html.Img(
src="./assets/images/logo.png",
style={"width": "100px"},
),
dmc.Text(
"OMERO Metrics Dashboard",
c=primary_color,
style={"fontSize": 15},
dmc.Title(
"PSF Beads Dashboard",
c="#189A35",
size="h3",
mb=10,
mt=5,
),
]
),
]
],
style={
"background-color": "white",
"border-radius": "0.5rem",
"padding": "10px",
},
),
dmc.Divider(variant="solid"),
dmc.Stack(
html.Div(
[
dmc.Flex(
children=[content, content, content],
direction={"base": "column", "sm": "row"},
gap={"base": "sm", "sm": "lg"},
justify={"sm": "space-between"},
align={"sm": "center"},
style={
"margin-top": "20px",
"margin-bottom": "10px",
},
),
dmc.Divider(variant="solid"),
dmc.Center(
dmc.Stack(
[
dmc.Title(
"Key Measurements",
c="#189A35",
size="h3",
mb=10,
dmc.Divider(variant="solid"),
dmc.Center(
[
dmc.Title(
"Key Measurements",
c="#189A35",
size="h3",
mb=10,
),
]
),
dmc.ScrollArea(
[
dmc.Table(
id="key_values_psf",
striped=True,
highlightOnHover=True,
className="table table-striped table-bordered",
styles={
"background-color": "white",
"width": "auto",
"height": "auto",
"overflow-X": "auto",
},
)
]
),
]
),
dmc.Table(
id="key_values_psf",
striped=True,
highlightOnHover=True,
className="table table-striped table-bordered",
styles={"background-color": "white"},
),
]
)
],
style={
"background-color": "white",
"border-radius": "0.5rem",
"padding": "10px",
},
),
dmc.Divider(variant="solid"),
html.Div(id="blank-input"),
],
fluid=True,
style={
"background-color": "#eceff1",
"margin": "20px",
"margin": "10px",
"border-radius": "0.5rem",
"padding": "10px",
},
Expand Down
Loading

0 comments on commit 15ae803

Please sign in to comment.