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feat(waveform1d): dap LMFit model can be added to plot

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This commit is contained in:
wyzula_j
2024-06-24 13:11:01 +02:00
parent 6175a04a90
commit 1866ba66c8
7 changed files with 246 additions and 27 deletions
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57
bec_widgets/cli/client.py
View File

@ -31,6 +31,13 @@ class BECCurve(RPCBase):
Remove the curve from the plot.
"""
@property
@rpc_call
def dap_params(self):
"""
None
"""
@property
@rpc_call
def rpc_id(self) -> "str":
@ -143,6 +150,13 @@ class BECCurve(RPCBase):
tuple[np.ndarray,np.ndarray]: X and Y data of the curve.
"""
@property
@rpc_call
def dap_params(self):
"""
None
"""
class BECDock(RPCBase):
@property
@ -457,6 +471,7 @@ class BECFigure(RPCBase):
row: "int" = None,
col: "int" = None,
config=None,
dap: "str | None" = None,
**axis_kwargs,
) -> "BECWaveform":
"""
@ -550,6 +565,7 @@ class BECFigure(RPCBase):
color_map_z: "str | None" = "plasma",
label: "str | None" = None,
validate: "bool" = True,
dap: "str | None" = None,
**axis_kwargs,
) -> "BECWaveform":
"""
@ -568,6 +584,7 @@ class BECFigure(RPCBase):
color_map_z(str): The color map to use for the z-axis.
label(str): The label of the curve.
validate(bool): If True, validate the device names and entries.
dap(str): The DAP model to use for the curve.
**axis_kwargs: Additional axis properties to set on the widget after creation.
Returns:
@ -1467,6 +1484,7 @@ class BECWaveform(RPCBase):
color_map_z: "str | None" = "plasma",
label: "str | None" = None,
validate: "bool" = True,
dap: "str | None" = None,
) -> "BECCurve":
"""
Plot a curve to the plot widget.
@ -1483,11 +1501,50 @@ class BECWaveform(RPCBase):
color_map_z(str): The color map to use for the z-axis.
label(str): The label of the curve.
validate(bool): If True, validate the device names and entries.
dap(str): The dap model to use for the curve. If not specified, none will be added.
Returns:
BECCurve: The curve object.
"""
@rpc_call
def add_dap(
self,
x_name: "str",
y_name: "str",
x_entry: "Optional[str]" = None,
y_entry: "Optional[str]" = None,
color: "Optional[str]" = None,
dap: "str" = "GaussianModel",
**kwargs,
) -> "BECCurve":
"""
Add LMFIT dap model curve to the plot widget.
Args:
x_name(str): Name of the x signal.
x_entry(str): Entry of the x signal.
y_name(str): Name of the y signal.
y_entry(str): Entry of the y signal.
color(str, optional): Color of the curve. Defaults to None.
color_map_z(str): The color map to use for the z-axis.
label(str, optional): Label of the curve. Defaults to None.
dap(str): The dap model to use for the curve.
**kwargs: Additional keyword arguments for the curve configuration.
Returns:
BECCurve: The curve object.
"""
@rpc_call
def get_dap_params(self) -> "dict":
"""
Get the DAP parameters of all DAP curves.
Returns:
dict: DAP parameters of all DAP curves.
"""
@rpc_call
def remove_curve(self, *identifiers):
"""

19
bec_widgets/examples/jupyter_console/jupyter_console_window.py
View File

@ -14,21 +14,6 @@ from bec_widgets.widgets.dock.dock_area import BECDockArea
from bec_widgets.widgets.figure import BECFigure
from bec_widgets.widgets.jupyter_console.jupyter_console import BECJupyterConsole
# class JupyterConsoleWidget(RichJupyterWidget): # pragma: no cover:
# def __init__(self):
# super().__init__()
#
# self.kernel_manager = QtInProcessKernelManager()
# self.kernel_manager.start_kernel(show_banner=False)
# self.kernel_client = self.kernel_manager.client()
# self.kernel_client.start_channels()
#
# self.kernel_manager.kernel.shell.push({"np": np, "pg": pg})
#
# def shutdown_kernel(self):
# self.kernel_client.stop_channels()
# self.kernel_manager.shutdown_kernel()
class JupyterConsoleWindow(QWidget): # pragma: no cover:
"""A widget that contains a Jupyter console linked to BEC Widgets with full API access (contains Qt and pyqtgraph API)."""
@ -61,6 +46,7 @@ class JupyterConsoleWindow(QWidget): # pragma: no cover:
"fig0": self.fig0,
"fig1": self.fig1,
"fig2": self.fig2,
"plt": self.plt,
"bar": self.bar,
}
)
@ -115,7 +101,8 @@ class JupyterConsoleWindow(QWidget): # pragma: no cover:
self.d2 = self.dock.add_dock(name="dock_2", position="bottom")
self.fig2 = self.d2.add_widget("BECFigure", row=0, col=0)
self.fig2.plot(x_name="samx", y_name="bpm4i")
self.plt = self.fig2.plot(x_name="samx", y_name="bpm3a")
self.plt.plot(x_name="samx", y_name="bpm4i", dap="GaussianModel")
self.bar = self.d2.add_widget("RingProgressBar", row=0, col=1)
self.bar.set_diameter(200)

1
bec_widgets/utils/bec_connector.py
View File

@ -228,6 +228,7 @@ class BECConnector:
all_connections = self.rpc_register.list_all_connections()
if len(all_connections) == 0:
print("No more connections. Shutting down GUI BEC client.")
self.bec_dispatcher.disconnect_all()
self.client.shutdown()
# def closeEvent(self, event):

19
bec_widgets/widgets/figure/figure.py
View File

@ -195,10 +195,11 @@ class BECFigure(BECConnector, pg.GraphicsLayoutWidget):
z_entry: str = None,
x: list | np.ndarray = None,
y: list | np.ndarray = None,
color: Optional[str] = None,
color_map_z: Optional[str] = "plasma",
label: Optional[str] = None,
color: str | None = None,
color_map_z: str | None = "plasma",
label: str | None = None,
validate: bool = True,
dap: str | None = None,
):
"""
Configure the waveform based on the provided parameters.
@ -217,6 +218,7 @@ class BECFigure(BECConnector, pg.GraphicsLayoutWidget):
color_map_z (str): The color map to use for the z-axis.
label (str): The label of the curve.
validate (bool): If True, validate the device names and entries.
dap (str): The DAP model to use for the curve.
"""
if x is not None and y is None:
if isinstance(x, np.ndarray):
@ -240,7 +242,7 @@ class BECFigure(BECConnector, pg.GraphicsLayoutWidget):
return waveform
# User wants to add scan curve -> 1D Waveform
if x_name is not None and y_name is not None and z_name is None and x is None and y is None:
waveform.add_curve_scan(
waveform.plot(
x_name=x_name,
y_name=y_name,
x_entry=x_entry,
@ -248,6 +250,7 @@ class BECFigure(BECConnector, pg.GraphicsLayoutWidget):
validate=validate,
color=color,
label=label,
dap=dap,
)
# User wants to add scan curve -> 2D Waveform Scatter
if (
@ -257,7 +260,7 @@ class BECFigure(BECConnector, pg.GraphicsLayoutWidget):
and x is None
and y is None
):
waveform.add_curve_scan(
waveform.plot(
x_name=x_name,
y_name=y_name,
z_name=z_name,
@ -268,6 +271,7 @@ class BECFigure(BECConnector, pg.GraphicsLayoutWidget):
color_map_z=color_map_z,
label=label,
validate=validate,
dap=dap,
)
# User wants to add custom curve
elif x is not None and y is not None and x_name is None and y_name is None:
@ -292,6 +296,7 @@ class BECFigure(BECConnector, pg.GraphicsLayoutWidget):
row: int = None,
col: int = None,
config=None,
dap: str | None = None,
**axis_kwargs,
) -> BECWaveform:
"""
@ -339,6 +344,7 @@ class BECFigure(BECConnector, pg.GraphicsLayoutWidget):
color_map_z=color_map_z,
label=label,
validate=validate,
dap=dap,
)
return waveform
@ -357,6 +363,7 @@ class BECFigure(BECConnector, pg.GraphicsLayoutWidget):
color_map_z: str | None = "plasma",
label: str | None = None,
validate: bool = True,
dap: str | None = None,
**axis_kwargs,
) -> BECWaveform:
"""
@ -375,6 +382,7 @@ class BECFigure(BECConnector, pg.GraphicsLayoutWidget):
color_map_z(str): The color map to use for the z-axis.
label(str): The label of the curve.
validate(bool): If True, validate the device names and entries.
dap(str): The DAP model to use for the curve.
**axis_kwargs: Additional axis properties to set on the widget after creation.
Returns:
@ -403,6 +411,7 @@ class BECFigure(BECConnector, pg.GraphicsLayoutWidget):
color_map_z=color_map_z,
label=label,
validate=validate,
dap=dap,
)
# TODO remove repetition from .plot method
return waveform

158
bec_widgets/widgets/figure/plots/waveform/waveform.py
View File

@ -1,10 +1,12 @@
from __future__ import annotations
import time
from collections import defaultdict
from typing import Any, Literal, Optional
import numpy as np
import pyqtgraph as pg
from bec_lib import messages
from bec_lib.endpoints import MessageEndpoints
from bec_lib.scan_data import ScanData
from pydantic import Field, ValidationError
@ -36,6 +38,8 @@ class BECWaveform(BECPlotBase):
"rpc_id",
"config_dict",
"plot",
"add_dap",
"get_dap_params",
"remove_curve",
"scan_history",
"curves",
@ -57,6 +61,7 @@ class BECWaveform(BECPlotBase):
"set_legend_label_size",
]
scan_signal_update = pyqtSignal()
dap_params_update = pyqtSignal(dict)
def __init__(
self,
@ -73,6 +78,7 @@ class BECWaveform(BECPlotBase):
)
self._curves_data = defaultdict(dict)
self.old_scan_id = None
self.scan_id = None
# Scan segment update proxy
@ -80,6 +86,9 @@ class BECWaveform(BECPlotBase):
self.scan_signal_update, rateLimit=25, slot=self._update_scan_segment_plot
)
self.proxy_update_dap = pg.SignalProxy(
self.scan_signal_update, rateLimit=25, slot=self.refresh_dap
)
# Get bec shortcuts dev, scans, queue, scan_storage, dap
self.get_bec_shortcuts()
@ -213,6 +222,7 @@ class BECWaveform(BECPlotBase):
color_map_z: str | None = "plasma",
label: str | None = None,
validate: bool = True,
dap: str | None = None, # TODO add dap custom curve wrapper
) -> BECCurve:
"""
Plot a curve to the plot widget.
@ -229,6 +239,7 @@ class BECWaveform(BECPlotBase):
color_map_z(str): The color map to use for the z-axis.
label(str): The label of the curve.
validate(bool): If True, validate the device names and entries.
dap(str): The dap model to use for the curve. If not specified, none will be added.
Returns:
BECCurve: The curve object.
@ -237,6 +248,8 @@ class BECWaveform(BECPlotBase):
if x is not None and y is not None:
return self.add_curve_custom(x=x, y=y, label=label, color=color)
else:
if dap:
self.add_dap(x_name=x_name, y_name=y_name, dap=dap)
return self.add_curve_scan(
x_name=x_name,
y_name=y_name,
@ -256,6 +269,7 @@ class BECWaveform(BECPlotBase):
y: list | np.ndarray,
label: str = None,
color: str = None,
curve_source: str = "custom",
**kwargs,
) -> BECCurve:
"""
@ -266,12 +280,13 @@ class BECWaveform(BECPlotBase):
y(list|np.ndarray): Y data of the curve.
label(str, optional): Label of the curve. Defaults to None.
color(str, optional): Color of the curve. Defaults to None.
curve_source(str, optional): Tag for source of the curve. Defaults to "custom".
**kwargs: Additional keyword arguments for the curve configuration.
Returns:
BECCurve: The curve object.
"""
curve_source = "custom"
curve_source = curve_source
curve_id = label or f"Curve {len(self.plot_item.curves) + 1}"
curve_exits = self._check_curve_id(curve_id, self._curves_data)
@ -314,10 +329,12 @@ class BECWaveform(BECPlotBase):
color_map_z: Optional[str] = "plasma",
label: Optional[str] = None,
validate_bec: bool = True,
source: str = "scan_segment",
dap: Optional[str] = None,
**kwargs,
) -> BECCurve:
"""
Add a curve to the plot widget from the scan segment.
Add a curve to the plot widget from the scan segment. #TODO adapt docs to DAP
Args:
x_name(str): Name of the x signal.
@ -335,7 +352,7 @@ class BECWaveform(BECPlotBase):
BECCurve: The curve object.
"""
# Check if curve already exists
curve_source = "scan_segment"
curve_source = source
# Get entry if not provided and validate
x_entry, y_entry, z_entry = self._validate_signal_entries(
@ -371,12 +388,74 @@ class BECWaveform(BECPlotBase):
x=SignalData(name=x_name, entry=x_entry),
y=SignalData(name=y_name, entry=y_entry),
z=SignalData(name=z_name, entry=z_entry) if z_name else None,
dap=dap,
),
**kwargs,
)
curve = self._add_curve_object(name=label, source=curve_source, config=curve_config)
return curve
def add_dap(
self,
x_name: str,
y_name: str,
x_entry: Optional[str] = None,
y_entry: Optional[str] = None,
color: Optional[str] = None,
dap: str = "GaussianModel",
**kwargs,
) -> BECCurve:
"""
Add LMFIT dap model curve to the plot widget.
Args:
x_name(str): Name of the x signal.
x_entry(str): Entry of the x signal.
y_name(str): Name of the y signal.
y_entry(str): Entry of the y signal.
color(str, optional): Color of the curve. Defaults to None.
color_map_z(str): The color map to use for the z-axis.
label(str, optional): Label of the curve. Defaults to None.
dap(str): The dap model to use for the curve.
**kwargs: Additional keyword arguments for the curve configuration.
Returns:
BECCurve: The curve object.
"""
x_entry, y_entry, _ = self._validate_signal_entries(
x_name, y_name, None, x_entry, y_entry, None
)
label = f"{y_name}-{y_entry}-{dap}"
curve = self.add_curve_scan(
x_name=x_name,
y_name=y_name,
x_entry=x_entry,
y_entry=y_entry,
color=color,
label=label,
source="DAP",
dap=dap,
pen_style="dash",
symbol="star",
**kwargs,
)
self.setup_dap(self.old_scan_id, self.scan_id)
self.refresh_dap()
return curve
def get_dap_params(self) -> dict:
"""
Get the DAP parameters of all DAP curves.
Returns:
dict: DAP parameters of all DAP curves.
"""
params = {}
for curve_id, curve in self._curves_data["DAP"].items():
params[curve_id] = curve.dap_params
return params
def _add_curve_object(
self,
name: str,
@ -528,13 +607,75 @@ class BECWaveform(BECPlotBase):
return
if current_scan_id != self.scan_id:
self.old_scan_id = self.scan_id
self.scan_id = current_scan_id
self.scan_segment_data = self.queue.scan_storage.find_scan_by_ID(
self.scan_id
) # TODO do scan access through BECFigure
self.setup_dap(self.old_scan_id, self.scan_id)
self.scan_signal_update.emit()
def setup_dap(self, old_scan_id, new_scan_id):
"""
Setup DAP for the new scan.
Args:
old_scan_id(str): old_scan_id, used to disconnect the previous dispatcher connection.
new_scan_id(str): new_scan_id, used to connect the new dispatcher connection.
"""
self.bec_dispatcher.disconnect_slot(
self.update_dap, MessageEndpoints.dap_response(old_scan_id)
)
if len(self._curves_data["DAP"]) > 0:
self.bec_dispatcher.connect_slot(
self.update_dap, MessageEndpoints.dap_response(new_scan_id)
)
def refresh_dap(self):
"""
Refresh the DAP curves with the latest data from the DAP model MessageEndpoints.dap_response().
"""
for curve_id, curve in self._curves_data["DAP"].items():
x_name = curve.config.signals.x.name
y_name = curve.config.signals.y.name
x_entry = curve.config.signals.x.entry
y_entry = curve.config.signals.y.entry
model_name = curve.config.signals.dap
model = getattr(self.dap, model_name)
msg = messages.DAPRequestMessage(
dap_cls="LmfitService1D",
dap_type="on_demand",
config={
"args": [self.scan_id, x_name, x_entry, y_name, y_entry],
"kwargs": {},
"class_args": model._plugin_info["class_args"],
"class_kwargs": model._plugin_info["class_kwargs"],
},
metadata={"RID": self.scan_id},
)
self.client.connector.set_and_publish(MessageEndpoints.dap_request(), msg)
@pyqtSlot(dict, dict)
def update_dap(self, msg, metadata):
self.msg = msg
scan_id, x_name, x_entry, y_name, y_entry = msg["dap_request"].content["config"]["args"]
model = msg["dap_request"].content["config"]["class_kwargs"]["model"]
curve_id_request = f"{y_name}-{y_entry}-{model}"
for curve_id, curve in self._curves_data["DAP"].items():
if curve_id == curve_id_request:
if msg["data"] is not None:
x = msg["data"][0]["x"]
y = msg["data"][0]["y"]
curve.setData(x, y)
curve.dap_params = msg["data"][1]["fit_parameters"]
self.dap_params_update.emit(curve.dap_params)
break
def _update_scan_segment_plot(self):
"""Update the plot with the data from the scan segment."""
data = self.scan_segment_data.data
@ -609,13 +750,17 @@ class BECWaveform(BECPlotBase):
if scan_index is not None and scan_id is not None:
raise ValueError("Only one of scan_id or scan_index can be provided.")
# Reset DAP connector
self.bec_dispatcher.disconnect_slot(
self.update_dap, MessageEndpoints.dap_response(self.scan_id)
)
if scan_index is not None:
self.scan_id = self.queue.scan_storage.storage[scan_index].scan_id
data = self.queue.scan_storage.find_scan_by_ID(self.scan_id).data
elif scan_id is not None:
self.scan_id = scan_id
data = self.queue.scan_storage.find_scan_by_ID(self.scan_id).data
self.setup_dap(self.old_scan_id, self.scan_id)
data = self.queue.scan_storage.find_scan_by_ID(self.scan_id).data
self._update_scan_curves(data)
def get_all_data(self, output: Literal["dict", "pandas"] = "dict") -> dict | pd.DataFrame:
@ -661,6 +806,9 @@ class BECWaveform(BECPlotBase):
def cleanup(self):
"""Cleanup the widget connection from BECDispatcher."""
self.bec_dispatcher.disconnect_slot(self.on_scan_segment, MessageEndpoints.scan_segment())
self.bec_dispatcher.disconnect_slot(
self.update_dap, MessageEndpoints.dap_response(self.scan_id)
)
for curve in self.curves:
curve.cleanup()
super().cleanup()

15
bec_widgets/widgets/figure/plots/waveform/waveform_curve.py
View File

@ -31,6 +31,7 @@ class Signal(BaseModel):
x: SignalData # TODO maybe add metadata for config gui later
y: SignalData
z: Optional[SignalData] = None
dap: Optional[str] = None
model_config: dict = {"validate_assignment": True}
@ -63,6 +64,7 @@ class CurveConfig(ConnectionConfig):
class BECCurve(BECConnector, pg.PlotDataItem):
USER_ACCESS = [
"remove",
"dap_params",
"rpc_id",
"config_dict",
"set",
@ -75,6 +77,7 @@ class BECCurve(BECConnector, pg.PlotDataItem):
"set_pen_width",
"set_pen_style",
"get_data",
"dap_params",
]
def __init__(
@ -96,6 +99,7 @@ class BECCurve(BECConnector, pg.PlotDataItem):
self.parent_item = parent_item
self.apply_config()
self.dap_params = None
if kwargs:
self.set(**kwargs)
@ -119,6 +123,14 @@ class BECCurve(BECConnector, pg.PlotDataItem):
self.setSymbolSize(self.config.symbol_size)
self.setSymbol(self.config.symbol)
@property
def dap_params(self):
return self._dap_params
@dap_params.setter
def dap_params(self, value):
self._dap_params = value
def set_data(self, x, y):
if self.config.source == "custom":
self.setData(x, y)
@ -241,5 +253,6 @@ class BECCurve(BECConnector, pg.PlotDataItem):
def remove(self):
"""Remove the curve from the plot."""
self.parent_item.removeItem(self)
# self.parent_item.removeItem(self)
self.parent_item.remove_curve(self.name())
self.cleanup()

4
tests/unit_tests/test_waveform1d.py
View File

@ -85,6 +85,7 @@ def test_create_waveform1D_by_config(bec_figure):
"pen_style": "dash",
"source": "scan_segment",
"signals": {
"dap": None,
"source": "scan_segment",
"x": {
"name": "samx",
@ -248,6 +249,7 @@ def test_change_curve_appearance_methods(bec_figure, qtbot):
assert c1.config.pen_style == "dashdot"
assert c1.config.source == "scan_segment"
assert c1.config.signals.model_dump() == {
"dap": None,
"source": "scan_segment",
"x": {"name": "samx", "entry": "samx", "unit": None, "modifier": None, "limits": None},
"y": {"name": "bpm4i", "entry": "bpm4i", "unit": None, "modifier": None, "limits": None},
@ -277,6 +279,7 @@ def test_change_curve_appearance_args(bec_figure):
assert c1.config.pen_style == "dashdot"
assert c1.config.source == "scan_segment"
assert c1.config.signals.model_dump() == {
"dap": None,
"source": "scan_segment",
"x": {"name": "samx", "entry": "samx", "unit": None, "modifier": None, "limits": None},
"y": {"name": "bpm4i", "entry": "bpm4i", "unit": None, "modifier": None, "limits": None},
@ -384,6 +387,7 @@ def test_curve_add_by_config(bec_figure):
"pen_style": "dash",
"source": "scan_segment",
"signals": {
"dap": None,
"source": "scan_segment",
"x": {"name": "samx", "entry": "samx", "unit": None, "modifier": None, "limits": None},
"y": {