Node store

.github/workflows/pin_requirements.yml

@@ -10,7 +10,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macOS-latest]
-        python-version: ["3.9", "3.10"]
+        python-version: ["3.10"]
     steps:
       - name: Checkout code
         uses: actions/checkout@v3

.github/workflows/pypi_main.yml

@@ -11,10 +11,10 @@ jobs:
       uses: actions/checkout@v3
       with:
         fetch-depth: 0
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v4
       with:
-        python-version: 3.9
+        python-version: "3.10"
     - name: Install Hatch
       run: pip install hatch
     - name: Build

.github/workflows/pypi_test.yml

@@ -11,10 +11,10 @@ jobs:
       uses: actions/checkout@v3
       with:
         fetch-depth: 0
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v4
       with:
-        python-version: 3.9
+        python-version: "3.10"
     - name: Install Hatch
       run: pip install hatch
     - name: Build

.github/workflows/pytest.yml

@@ -7,7 +7,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ "ubuntu-latest", "macos-latest" , "windows-latest"]
-        python-version: ["3.9", "3.10" ]
+        python-version: ["3.10" ]
     defaults:
       run:
         shell: bash

dont_fret/config/config.py

@@ -28,6 +28,7 @@ class BurstFilterItem:
     name: str
     min: Optional[float] = field(default=None)
     max: Optional[float] = field(default=None)
+    active: bool = field(default=True)
 
     def as_expr(self) -> list[pl.Expr]:
         expr = []

dont_fret/models.py

@@ -73,6 +73,11 @@ def cps(self) -> float:
         """Average count rate (counts per second / Hz)"""
         return len(self) / float(self.photon_times.max())  # type: ignore
 
+    @property
+    def duration(self) -> Optional[float]:
+        """user-specified duration in seconds, obtained from metadata"""
+        return self.metadata.get("acquisition_duration")
+
     def __getitem__(self, key):
         # TODO sort when slicing backwards?
         return self.__class__(self.data[key], metadata=self.metadata, cfg=self.cfg)
@@ -132,7 +137,7 @@ def nanotimes_unit(self) -> Optional[float]:
     def tau_mean(self) -> float:
         """Mean of the nanotimes (in seconds). Sometimes referred to as 'fast lifetime' as it is fast to compute"""
         if self.nanotimes is not None and self.nanotimes_unit is not None:
-            return self.nanotimes.mean() * self.nanotimes_unit
+            return self.nanotimes.mean() * self.nanotimes_unit  # type: ignore
         else:
             return np.nan
 
@@ -365,10 +370,16 @@ def __init__(
         self.metadata: dict = metadata or {}
         self.cfg = cfg
 
+        # number of photons per stream per burst
         agg = [(pl.col("stream") == stream).sum().alias(f"n_{stream}") for stream in cfg.streams]
+
+        # mean nanotimes per stream per burst
         agg.extend(
             [
-                pl.when(pl.col("stream") == k).then(pl.col("nanotimes")).mean().alias(f"tau_{k}")
+                pl.when(pl.col("stream") == k)
+                .then(pl.col("nanotimes"))
+                .mean()
+                .alias(f"nanotimes_{k}")
                 for k in cfg.streams
             ]
         )
@@ -387,6 +398,8 @@ def __init__(
             photon_data["burst_index"].unique_counts().alias("n_photons"),
         ]
 
+        # TODO These should move somewhere else; possibly some second step conversion
+        # from raw stamps to times
         t_unit = self.metadata.get("timestamps_unit", None)
         if t_unit is not None:
             columns.extend(
@@ -397,6 +410,14 @@ def __init__(
                     ),
                 ]
             )
+        nanotimes_unit = self.metadata.get("nanotimes_unit", None)
+        if nanotimes_unit is not None:
+            columns.extend(
+                [
+                    pl.col(f"nanotimes_{stream}").mul(nanotimes_unit).alias(f"tau_{stream}")
+                    for stream in cfg.streams
+                ]
+            )
 
         self.burst_data = (
             self.photon_data.group_by("burst_index", maintain_order=True)

dont_fret/process.py

@@ -41,7 +41,7 @@ def search_and_save(
 
 
 def write_dataframe(df: pl.DataFrame, path: Path) -> None:
-    """Write a dataframe to disk. Writier used depends on path suffix."""
+    """Write a dataframe to disk. Writer used depends on path suffix."""
     if path.suffix == ".pq":
         df.write_parquet(path)
     elif path.suffix == ".csv":

dont_fret/tmp.py

@@ -1,51 +1,53 @@
+import uuid
+from dataclasses import replace
+from functools import reduce
+from itertools import chain
+from operator import and_
 from pathlib import Path
+from typing import Callable, Dict, List, Optional, Type, TypedDict, Union
 
+import altair as alt
+import numpy as np
 import solara
 import solara.lab
 import yaml
 
 import dont_fret.web.state as state
-from dont_fret.config.config import cfg
-from dont_fret.web.dev import load_burst_items, load_file_items
+from dont_fret.config.config import BurstFilterItem, cfg
+from dont_fret.web.bursts import BurstPage
+from dont_fret.web.bursts.components import BurstFigure, BurstFigureSelection
+from dont_fret.web.components import RegexSelectDialog
 from dont_fret.web.home import HomePage
 from dont_fret.web.main import Page as MainPage
-from dont_fret.web.models import FRETNode
+from dont_fret.web.models import BurstNode, ListStore, PhotonNode
+from dont_fret.web.trace import TracePage
+from dont_fret.web.utils import (
+    find_index,
+    find_object,
+    get_bursts,
+    make_selector_nodes,
+    wrap_callback,
+)
 
 data = yaml.safe_load(Path("default_testing.yaml").read_text())
 cfg.update(data)
 
+style = """
+.vega-embed {
+    overflow: visible;
+    width: 100% !important;
+}
+"""
 
-# TODO default burst searches from config
-DCBS_TEST = {"DD + DA": {"L": 50, "M": 35, "T": 0.0005}, "AA": {"L": 50, "M": 35, "T": 0.0005}}
-APBS_TEST = {"DD + DA + AA": {"L": 50, "M": 35, "T": 0.0005}}
+my_selection = ListStore([])
 
-pth = "ds2"
-photon_file_items = load_file_items(pth)
-# burst_items = load_burst_items(pth, suffix=".csv")
+values = ["a", "b1", "c1", "d3"]
 
-fret_nodes = [
-    FRETNode(
-        name="FRET NOT",
-        photons=photon_file_items,
-        # bursts=burst_items,
-    ),
-]
-
-# %%
+state.disable_burst_page.set(False)
+state.disable_trace_page.set(False)
 
 
 @solara.component
 def Page():
-    def preload():
-        # state.FRET_NODES.set([])
-        if len(state.fret_nodes.value) == 0:
-            state.fret_nodes.extend(fret_nodes)
-
-    solara.use_effect(preload, dependencies=[])
-    nodes = state.fret_nodes.value
-
-    if len(nodes) != 0:
-        with solara.Column(style={"height": "100%"}):
-            MainPage()
-    else:
-        solara.Text("Loading fret nodes...")
+    solara.Style(style)
+    MainPage()