remove empty pulses from timed dataframe, and bring back old behavior

OpenCOMPES · Jan 6, 2025 · 8d9bcd5 · 8d9bcd5
1 parent 178c6ea
commit 8d9bcd5
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Showing 4 changed files with 6 additions and 6 deletions.
diff --git a/src/sed/loader/flash/buffer_handler.py b/src/sed/loader/flash/buffer_handler.py
@@ -187,7 +187,7 @@ def _save_buffer_file(self, paths: dict[str, Path]) -> None:
 
         # timed dataframe
         # drop the electron channels and only take rows with the first electronId
-        df_timed = df[self.fill_channels].loc[:, :, 0]
+        df_timed = df.dropna(subset=electron_channels)[self.fill_channels].loc[:, :, 0]
         dtypes = get_dtypes(self._config, df_timed.columns.values)
         df_timed.astype(dtypes).reset_index().to_parquet(paths["timed"])
         logger.debug(f"Processed {paths['raw'].stem}")

diff --git a/tutorial/10_hextof_workflow_trXPS_bam_correction.ipynb b/tutorial/10_hextof_workflow_trXPS_bam_correction.ipynb
@@ -228,7 +228,7 @@
     "axes = ['energy', 'delayStage']\n",
     "ranges = [[-37.5,-27.5], [1446.75,1449.15]]\n",
     "bins = [200,40]\n",
-    "res = sp_44498.compute(bins=bins, axes=axes, ranges=ranges)"
+    "res = sp_44498.compute(bins=bins, axes=axes, ranges=ranges, normalize_to_acquisition_time=\"delayStage\")"
    ]
   },
   {
@@ -394,7 +394,7 @@
     "axes = ['energy', 'delayStage']\n",
     "ranges = [[-37.5,-27.5], [-1.5,1.5]]\n",
     "bins = [200,60]\n",
-    "res_corr = sp_44498.compute(bins=bins, axes=axes, ranges=ranges)"
+    "res_corr = sp_44498.compute(bins=bins, axes=axes, ranges=ranges, normalize_to_acquisition_time=\"delayStage\")"
    ]
   },
   {

diff --git a/tutorial/11_hextof_workflow_trXPS_energy_calibration_using_SB.ipynb b/tutorial/11_hextof_workflow_trXPS_energy_calibration_using_SB.ipynb
@@ -325,7 +325,7 @@
     "axes = ['dldTimeSteps', 'delayStage']\n",
     "ranges = [[3900,4200], [-1.5,1.5]]\n",
     "bins = [100,60]\n",
-    "res_corr = sp_44498.compute(bins=bins, axes=axes, ranges=ranges)\n",
+    "res_corr = sp_44498.compute(bins=bins, axes=axes, ranges=ranges, normalize_to_acquisition_time=\"delayStage\")\n",
     "\n",
     "fig,ax = plt.subplots(1,2,figsize=(8,3), layout='constrained')\n",
     "fig.suptitle(f\"Run {run_number}: W 4f, side bands\")\n",
@@ -441,7 +441,7 @@
     "axes = ['energy', 'delayStage']\n",
     "ranges = [[-37.5,-27.5], [-1.5,1.5]]\n",
     "bins = [200,60]\n",
-    "res_corr = sp_44498.compute(bins=bins, axes=axes, ranges=ranges)\n",
+    "res_corr = sp_44498.compute(bins=bins, axes=axes, ranges=ranges, normalize_to_acquisition_time=\"delayStage\")\n",
     "\n",
     "fig,ax = plt.subplots(1,2,figsize=(8,3), layout='constrained')\n",
     "fig.suptitle(f\"Run {run_number}: W 4f, side bands\")\n",

diff --git a/tutorial/9_hextof_workflow_trXPD.ipynb b/tutorial/9_hextof_workflow_trXPD.ipynb
@@ -281,7 +281,7 @@
     "axes = ['energy', 'delayStage']\n",
     "ranges = [[-37.5,-27.5], [-1.5,1.5]]\n",
     "bins = [200,60]\n",
-    "res_corr = sp_44498.compute(bins=bins, axes=axes, ranges=ranges)"
+    "res_corr = sp_44498.compute(bins=bins, axes=axes, ranges=ranges, normalize_to_acquisition_time=\"delayStage\")"
    ]
   },
   {