Update pynxtools

pyproject.toml

@@ -29,7 +29,7 @@ classifiers = [
     "Operating System :: OS Independent",
 ]
 dependencies = [
-    "bokeh>=2.4.2,<3.7.0",
+    "bokeh>=2.4.2",
     "dask>=2021.12.0,<2024.8",
     "elabapi-python>=5.0,<5.2",
     "fastdtw>=0.3.4",

src/sed/binning/binning.py

@@ -121,11 +121,14 @@ def bin_partition(
 
     # convert bin centers to bin edges:
     if all(isinstance(x, np.ndarray) for x in bins):
-        bins = cast(list[np.ndarray], bins)
+        # create a copy to avoid modifying input data
+        bins = list(cast(list[np.ndarray], bins))
         for i, bin_centers in enumerate(bins):
             bins[i] = bin_centers_to_bin_edges(bin_centers)
     else:
         bins = cast(list[int], bins)
+        # create a copy to avoid modifying input data
+        ranges = list(ranges)
         # shift ranges by half a bin size to align the bin centers to the given ranges,
         # as the histogram functions interpret the ranges as limits for the edges.
         for i, nbins in enumerate(bins):

src/sed/calibrator/energy.py

@@ -734,8 +734,8 @@ def view(
                 title=ttl,
                 width=figsize[0] * 100,
                 height=figsize[1] * 100,
-                tooltips=ttp,
             )
+            fig.hover.tooltips = ttp
             # Plotting the main traces
             for itr, color in zip(range(len(traces)), colors):
                 trace = traces[itr, :]
@@ -790,7 +790,7 @@ def view(
             if show_legend:
                 fig.legend.location = kwds.pop("legend_location", "top_right")
                 fig.legend.spacing = 0
-                fig.legend.padding = 2
+                fig.legend.padding = 2  # type: ignore
 
             pbk.show(fig)
 

src/sed/calibrator/momentum.py

@@ -21,6 +21,7 @@
 import xarray as xr
 from bokeh.colors import RGB
 from bokeh.io import output_notebook
+from bokeh.models import Range1d
 from bokeh.palettes import Category10 as ColorCycle
 from IPython.display import display
 from joblib import delayed
@@ -1408,10 +1409,10 @@ def view(
             fig = pbk.figure(
                 width=figsize[0] * 100,
                 height=figsize[1] * 100,
-                tooltips=ttp,
-                x_range=(0, num_rows),
-                y_range=(0, num_cols),
+                x_range=Range1d(0, num_rows),
+                y_range=Range1d(0, num_cols),
             )
+            fig.hover.tooltips = ttp
             fig.image(
                 image=[image.T],
                 x=0,
@@ -1832,11 +1833,11 @@ def gather_correction_metadata(self) -> dict:
             metadata["registration"]["creation_date"] = datetime.now()
             metadata["registration"]["applied"] = True
             metadata["registration"]["depends_on"] = (
-                "/entry/process/registration/transformations/rot_z"
+                "/entry/registration/transformations/rot_z"
                 if "angle" in metadata["registration"] and metadata["registration"]["angle"]
-                else "/entry/process/registration/transformations/trans_y"
+                else "/entry/registration/transformations/trans_y"
                 if "xtrans" in metadata["registration"] and metadata["registration"]["xtrans"]
-                else "/entry/process/registration/transformations/trans_x"
+                else "/entry/registration/transformations/trans_x"
                 if "ytrans" in metadata["registration"] and metadata["registration"]["ytrans"]
                 else "."
             )
@@ -1860,7 +1861,7 @@ def gather_correction_metadata(self) -> dict:
                     [0.0, 1.0, 0.0],
                 )
                 metadata["registration"]["trans_y"]["depends_on"] = (
-                    "/entry/process/registration/transformations/trans_x"
+                    "/entry/registration/transformations/trans_x"
                     if "ytrans" in metadata["registration"] and metadata["registration"]["ytrans"]
                     else "."
                 )
@@ -1875,10 +1876,11 @@ def gather_correction_metadata(self) -> dict:
                 metadata["registration"]["rot_z"]["offset"] = np.concatenate(
                     (metadata["registration"]["center"], [0.0]),
                 )
+                metadata["registration"]["rot_z"]["offset_units"] = "pixel"
                 metadata["registration"]["rot_z"]["depends_on"] = (
-                    "/entry/process/registration/transformations/trans_y"
+                    "/entry/registration/transformations/trans_y"
                     if "xtrans" in metadata["registration"] and metadata["registration"]["xtrans"]
-                    else "/entry/process/registration/transformations/trans_x"
+                    else "/entry/registration/transformations/trans_x"
                     if "ytrans" in metadata["registration"] and metadata["registration"]["ytrans"]
                     else "."
                 )

src/sed/config/NXmpes_config.json

@@ -296,7 +296,7 @@
   },
   "/ENTRY/REGISTRATION[registration]": {
     "applied": "!@attrs:metadata/momentum_correction/registration/applied",
-    "depends_on": "/entry/process/registration/transformations/rot_z",
+    "depends_on": "/entry/registration/transformations/rot_z",
     "TRANSFORMATIONS[transformations]": {
       "AXISNAME[trans_x]": "@attrs:metadata/momentum_correction/registration/trans_x/value",
       "AXISNAME[trans_x]/@transformation_type": "translation",

src/sed/diagnostics.py

@@ -34,7 +34,8 @@ def plot_single_hist(
     """
     ttp = kwds.pop("tooltip", [("(x, y)", "($x, $y)")])
 
-    fig = pbk.figure(background_fill_color="white", tooltips=ttp)
+    fig = pbk.figure(background_fill_color="white")
+    fig.hover.tooltips = ttp
     fig.quad(
         top=histvals,
         bottom=0,

tests/calibrator/test_momentum.py

@@ -239,44 +239,44 @@ def test_apply_correction() -> None:
 ]
 depends_on_list = [
     {
-        "root": "/entry/process/registration/transformations/trans_x",
+        "root": "/entry/registration/transformations/trans_x",
         "axes": {"trans_x": "."},
     },
     {
-        "root": "/entry/process/registration/transformations/trans_y",
+        "root": "/entry/registration/transformations/trans_y",
         "axes": {"trans_y": "."},
     },
     {
-        "root": "/entry/process/registration/transformations/rot_z",
+        "root": "/entry/registration/transformations/rot_z",
         "axes": {"rot_z": "."},
     },
     {
-        "root": "/entry/process/registration/transformations/trans_y",
+        "root": "/entry/registration/transformations/trans_y",
         "axes": {
             "trans_x": ".",
-            "trans_y": "/entry/process/registration/transformations/trans_x",
+            "trans_y": "/entry/registration/transformations/trans_x",
         },
     },
     {
-        "root": "/entry/process/registration/transformations/rot_z",
+        "root": "/entry/registration/transformations/rot_z",
         "axes": {
             "trans_x": ".",
-            "rot_z": "/entry/process/registration/transformations/trans_x",
+            "rot_z": "/entry/registration/transformations/trans_x",
         },
     },
     {
-        "root": "/entry/process/registration/transformations/rot_z",
+        "root": "/entry/registration/transformations/rot_z",
         "axes": {
             "trans_y": ".",
-            "rot_z": "/entry/process/registration/transformations/trans_y",
+            "rot_z": "/entry/registration/transformations/trans_y",
         },
     },
     {
-        "root": "/entry/process/registration/transformations/rot_z",
+        "root": "/entry/registration/transformations/rot_z",
         "axes": {
             "trans_x": ".",
-            "trans_y": "/entry/process/registration/transformations/trans_x",
-            "rot_z": "/entry/process/registration/transformations/trans_y",
+            "trans_y": "/entry/registration/transformations/trans_x",
+            "rot_z": "/entry/registration/transformations/trans_y",
         },
     },
 ]

tests/test_dfops.py

@@ -160,7 +160,7 @@ def swap(x, y):
 def test_forward_fill_lazy_sparse_nans() -> None:
     """test that a lazy forward fill works as expected with sparse nans"""
     t_df = df.copy()
-    t_df["energy"][::2] = np.nan
+    t_df.iloc[::2, 2] = np.nan
     t_dask_df = ddf.from_pandas(t_df, npartitions=N_PARTITIONS)
     t_dask_df = forward_fill_lazy(t_dask_df, "energy", before="max")
     t_df = t_df.ffill()
@@ -170,7 +170,7 @@ def test_forward_fill_lazy_sparse_nans() -> None:
 def test_forward_fill_lazy_full_partition_nans() -> None:
     """test that a lazy forward fill works as expected with a full partition of nans"""
     t_df = df.copy()
-    t_df["energy"][5:25] = np.nan
+    t_df.iloc[5:25, 2] = np.nan
     t_dask_df = ddf.from_pandas(t_df, npartitions=N_PARTITIONS)
     t_dask_df = forward_fill_lazy(t_dask_df, "energy", before="max")
     t_df = t_df.ffill()
@@ -182,7 +182,7 @@ def test_forward_fill_lazy_consecutive_full_partition_nans() -> None:
     full of nans
     """
     t_df = df.copy()
-    t_df["energy"][5:35] = np.nan
+    t_df.iloc[5:35, 2] = np.nan
     t_dask_df = ddf.from_pandas(t_df, npartitions=N_PARTITIONS)
     t_dask_df = forward_fill_lazy(t_dask_df, "energy", before="max")
     t_df = t_df.ffill()
@@ -192,7 +192,7 @@ def test_forward_fill_lazy_consecutive_full_partition_nans() -> None:
 def test_forward_fill_lazy_wrong_parameters() -> None:
     """test that a lazy forward fill fails as expected on wrong parameters"""
     t_df = df.copy()
-    t_df["energy"][5:35] = np.nan
+    t_df.iloc[5:35, 2] = np.nan
     t_dask_df = ddf.from_pandas(t_df, npartitions=N_PARTITIONS)
     with pytest.raises(TypeError):
         t_dask_df = forward_fill_lazy(t_dask_df, "energy", before="wrong parameter")
@@ -201,7 +201,7 @@ def test_forward_fill_lazy_wrong_parameters() -> None:
 def test_forward_fill_lazy_compute() -> None:
     """test that a lazy forward fill works as expected with compute=True"""
     t_df = df.copy()
-    t_df["energy"][5:35] = np.nan
+    t_df.iloc[5:35, 2] = np.nan
     t_dask_df = ddf.from_pandas(t_df, npartitions=N_PARTITIONS)
     t_dask_df_comp = forward_fill_lazy(t_dask_df, "energy", before="max", compute_lengths=True)
     t_dask_df_nocomp = forward_fill_lazy(t_dask_df, "energy", before="max", compute_lengths=False)
@@ -212,7 +212,7 @@ def test_forward_fill_lazy_keep_head_nans() -> None:
     """test that a lazy forward fill works as expected with missing values at the
     beginning of the dataframe"""
     t_df = df.copy()
-    t_df["energy"][:5] = np.nan
+    t_df.iloc[:5, 2] = np.nan
     t_dask_df = ddf.from_pandas(t_df, npartitions=N_PARTITIONS)
     t_df = forward_fill_lazy(t_dask_df, "energy", before="max").compute()
     assert np.all(np.isnan(t_df["energy"][:5]))
@@ -238,7 +238,7 @@ def test_forward_fill_lazy_wrong_channels() -> None:
 def test_forward_fill_lazy_multiple_iterations() -> None:
     """test that a lazy forward fill works as expected with multiple iterations"""
     t_df = df.copy()
-    t_df["energy"][5:35] = np.nan
+    t_df.loc[5:35, "energy"] = np.nan
     t_dask_df = ddf.from_pandas(t_df, npartitions=N_PARTITIONS)
     t_dask_df = forward_fill_lazy(t_dask_df, "energy", before="max", iterations=5)
     t_df = t_df.ffill()