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Re-factored the run browser into its own sub-package within Firefly.
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@canismarko
canismarko committed Oct 27, 2024
1 parent 6af6fe8 commit 7e53ad2
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Showing 11 changed files with 384 additions and 983 deletions.
1 change: 1 addition & 0 deletions pytest.ini
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Expand Up @@ -5,3 +5,4 @@ asyncio_mode = auto
testpaths =
src/haven/tests
src/firefly/tests
src/firefly/run_browser/tests
Empty file added src/firefly/run_browser/__init__.py
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6 changes: 2 additions & 4 deletions src/firefly/run_client.py → src/firefly/run_browser/client.py
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
import datetime as dt
import logging
import warnings
from collections import OrderedDict
from typing import Mapping, Sequence
import warnings

import numpy as np
import pandas as pd
Expand Down Expand Up @@ -52,9 +52,7 @@ async def filtered_nodes(self, filters: Mapping):
return runs

async def load_distinct_fields(self):
"""Get distinct metadata fields for filterable metadata.
"""
"""Get distinct metadata fields for filterable metadata."""
new_fields = {}
target_fields = [
"sample_name",
Expand Down
274 changes: 13 additions & 261 deletions src/firefly/run_browser.py → src/firefly/run_browser/display.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,27 +3,21 @@
from collections import Counter
from contextlib import contextmanager
from functools import wraps
from itertools import count
from typing import Mapping, Optional, Sequence

import numpy as np
import qtawesome as qta
import yaml
from matplotlib.colors import TABLEAU_COLORS
from pandas.api.types import is_numeric_dtype
from pyqtgraph import GraphicsLayoutWidget, ImageView, PlotItem, PlotWidget
from qasync import asyncSlot
from qtpy.QtCore import Qt, Signal
from qtpy.QtGui import QStandardItem, QStandardItemModel
from qtpy.QtWidgets import QFileDialog, QWidget
from qtpy.QtWidgets import QWidget

from firefly import display
from firefly.run_client import DatabaseWorker

log = logging.getLogger(__name__)

from .client import DatabaseWorker
from .widgets import ExportDialog

colors = list(TABLEAU_COLORS.values())
log = logging.getLogger(__name__)


def cancellable(fn):
Expand All @@ -37,220 +31,6 @@ async def inner(*args, **kwargs):
return inner


class ExportDialog(QFileDialog):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.setFileMode(QFileDialog.FileMode.AnyFile)
self.setAcceptMode(QFileDialog.AcceptSave)

def ask(self, mimetypes: Optional[Sequence[str]] = None):
"""Get the name of the file to save for exporting."""
self.setMimeTypeFilters(mimetypes)
# Show the file dialog
if self.exec_() == QFileDialog.Accepted:
return self.selectedFiles()
else:
return None


class FiltersWidget(QWidget):
returnPressed = Signal()

def keyPressEvent(self, event):
super().keyPressEvent(event)
# Check for return keys pressed
if event.key() in [Qt.Key_Enter, Qt.Key_Return]:
self.returnPressed.emit()


class Browser1DPlotItem(PlotItem):
hover_coords_changed = Signal(str)

def hoverEvent(self, event):
super().hoverEvent(event)
if event.isExit():
self.hover_coords_changed.emit("NaN")
return
# Get data coordinates from event
pos = event.scenePos()
data_pos = self.vb.mapSceneToView(pos)
pos_str = f"({data_pos.x():.3f}, {data_pos.y():.3f})"
self.hover_coords_changed.emit(pos_str)


class BrowserMultiPlotWidget(GraphicsLayoutWidget):
_multiplot_items: Mapping

def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self._multiplot_items = {}

def multiplot_items(self, n_cols: int = 3):
view = self
item0 = None
for idx in count():
row = int(idx / n_cols)
col = idx % n_cols
# Make a new plot item if one doesn't exist
if (row, col) not in self._multiplot_items:
self._multiplot_items[(row, col)] = view.addPlot(row=row, col=col)
new_item = self._multiplot_items[(row, col)]
# Link the X-axes together
if item0 is None:
item0 = new_item
else:
new_item.setXLink(item0)
# Resize the viewing area to fit the contents
width = view.width()
plot_width = width / n_cols
# view.resize(int(width), int(plot_width * row))
view.setFixedHeight(1200)
yield new_item

def plot_runs(self, runs: Mapping, xsignal: str):
"""Take loaded run data and plot small multiples.
Parameters
==========
runs
Dictionary with pandas series for each curve. The keys
should be the curve labels, the series' indexes are the x
values and the series' values are the y data.
xsignal
The name of the signal to use for the common horizontal
axis.
"""
# Use all the data columns as y signals
ysignals = []
for run in runs.values():
ysignals.extend(run.columns)
# Remove the x-signal from the list of y signals
ysignals = sorted(list(dict.fromkeys(ysignals)))
# Plot the runs
self.clear()
self._multiplot_items = {}
for label, data in runs.items():
# Figure out which signals to plot
try:
xdata = data[xsignal]
except KeyError:
log.warning(f"Cannot plot x='{xsignal}' for {list(data.keys())}")
continue
# Plot each y signal on a separate plot
for ysignal, plot_item in zip(ysignals, self.multiplot_items()):
try:
if is_numeric_dtype(data[ysignal]):
plot_item.plot(xdata, data[ysignal])
except KeyError:
log.warning(f"No signal {ysignal} in data.")
else:
log.debug(f"Plotted {ysignal} vs. {xsignal} for {data}")
plot_item.setTitle(ysignal)


class Browser1DPlotWidget(PlotWidget):
cursor_needed: bool
data_items: dict

def __init__(self, parent=None, background="default", plotItem=None, **kargs):
plot_item = Browser1DPlotItem(**kargs)
super().__init__(parent=parent, background=background, plotItem=plot_item)
self.clear_runs()

def clear_runs(self):
self.getPlotItem().clear()
self.cursor_needed = True
self.data_items = {}

def plot_runs(self, runs: Mapping, ylabel="", xlabel=""):
"""Take loaded run data and plot it.
Parameters
==========
runs
Dictionary with pandas series for each curve. The keys
should be the curve labels, the series' indexes are the x
values and the series' values are the y data.
"""
plot_item = self.getPlotItem()
# Plot this run's data
for idx, (label, series) in enumerate(runs.items()):
color = colors[idx % len(colors)]
if label in self.data_items.keys():
# We've plotted this item before, so reuse it
data_item = self.data_items[label]
data_item.setData(series.index, series.values)
else:
self.data_items[label] = plot_item.plot(
x=series.index,
y=series.values,
pen=color,
name=label,
clear=False,
)
# Cursor to drag around on the data
if self.cursor_needed:
plot_item.addLine(
x=np.median(series.index), movable=True, label="{value:.3f}"
)
self.cursor_needed = False
# Axis formatting
plot_item.setLabels(left=ylabel, bottom=xlabel)


class Browser2DPlotWidget(ImageView):
"""A plot widget for 2D maps."""

def __init__(self, *args, view=None, **kwargs):
if view is None:
view = PlotItem()
super().__init__(*args, view=view, **kwargs)

def plot_runs(
self, runs: Mapping, xlabel: str = "", ylabel: str = "", extents=None
):
"""Take loaded 2D or 3D mapping data and plot it.
Parameters
==========
runs
Dictionary with pandas series for each curve. The keys
should be the curve labels, the series' indexes are the x
values and the series' values are the y data.
xlabel
The label for the horizontal axis.
ylabel
The label for the vertical axis.
extents
Spatial extents for the map as ((-y, +y), (-x, +x)).
"""
images = np.asarray(list(runs.values()))
# Combine the different runs into one image
# To-do: make this respond to the combobox selection
image = np.mean(images, axis=0)
# To-do: Apply transformations

# # Plot the image
if 2 <= image.ndim <= 3:
self.setImage(image.T, autoRange=False)
else:
log.info(f"Could not plot image of dataset with shape {image.shape}.")
return
# Determine the axes labels
self.view.setLabel(axis="bottom", text=xlabel)
self.view.setLabel(axis="left", text=ylabel)
# Set axes extent
yextent, xextent = extents
x = xextent[0]
y = yextent[0]
w = xextent[1] - xextent[0]
h = yextent[1] - yextent[0]
self.getImageItem().setRect(x, y, w, h)


class RunBrowserDisplay(display.FireflyDisplay):
runs_model: QStandardItemModel
_run_col_names: Sequence = [
Expand Down Expand Up @@ -651,6 +431,7 @@ async def update_metadata(self, *args):
text += yaml.dump(md)
text += f"\n\n{'=' * 20}\n\n"
# Update the widget with the rendered metadata
print(text)
self.ui.metadata_textedit.document().setPlainText(text)

def clear_plots(self):
Expand All @@ -659,39 +440,36 @@ def clear_plots(self):
If a *uid* is provided, only the plots matching the scan with
*uid* will be updated.
"""
self.plot_1d_view.clear_plots()
self.plot_1d_view.clear_runs()

@asyncSlot()
@cancellable
async def update_plots(self, uid: str = ""):
async def update_plots(self):
"""Get new data, and update all the plots.
If a *uid* is provided, only the plots matching the scan with
*uid* will be updated.
"""

asyncio.gather(
await asyncio.gather(
self.update_metadata(),
self.update_1d_plot(uid=uid),
self.update_1d_plot(),
self.update_2d_plot(),
self.update_multi_plot(),
)

@asyncSlot()
@cancellable
async def update_selected_runs(self, uid=None, *args):

"""Get the current runs from the database and stash them.
"""
async def update_selected_runs(self, *args):
"""Get the current runs from the database and stash them."""
# Get UID's from the selection
col_idx = self._run_col_names.index("UID")
indexes = self.ui.run_tableview.selectedIndexes()
uids = [i.siblingAtColumn(col_idx).data() for i in indexes]
# Get selected runs from the database
with self.busy_hints(run_widgets=True, run_table=False, filter_widgets=False):
task = self.db_task(
self.db.load_selected_runs(uids), "update selected runs"
self.db.load_selected_runs(uids=uids), "update selected runs"
)
self.selected_runs = await task
# Update the necessary UI elements
Expand Down Expand Up @@ -731,30 +509,4 @@ def load_models(self):
self.ui.run_tableview.setModel(self.runs_model)

def ui_filename(self):
return "run_browser.ui"


# -----------------------------------------------------------------------------
# :author: Mark Wolfman
# :email: [email protected]
# :copyright: Copyright © 2023, UChicago Argonne, LLC
#
# Distributed under the terms of the 3-Clause BSD License
#
# The full license is in the file LICENSE, distributed with this software.
#
# DISCLAIMER
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# -----------------------------------------------------------------------------
return "run_browser/run_browser.ui"
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