jolly-roger 0.2.0__tar.gz → 0.3.0__tar.gz

{jolly_roger-0.2.0 → jolly_roger-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: jolly-roger
-Version: 0.2.0
+Version: 0.3.0
 Summary: The pirate flagger
 Project-URL: Homepage, https://github.com/flint-crew/jolly-roger
 Project-URL: Bug Tracker, https://github.com/flint-crew/jolly-roger/issues

{jolly_roger-0.2.0 → jolly_roger-0.3.0}/jolly_roger/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.2.0'
-__version_tuple__ = version_tuple = (0, 2, 0)
+__version__ = version = '0.3.0'
+__version_tuple__ = version_tuple = (0, 3, 0)

{jolly_roger-0.2.0 → jolly_roger-0.3.0}/jolly_roger/plots.py

@@ -85,15 +85,17 @@ def plot_baseline_comparison_data(
         norm = ImageNormalize(
             after_amp_stokesi, interval=ZScaleInterval(), stretch=SqrtStretch()
         )
+        cmap = plt.cm.viridis
 
         fig, ((ax1, ax2), (ax3, ax4)) = plt.subplots(
-            2, 2, figsize=(10, 10), sharex=True, sharey="row"
+            2, 2, figsize=(12, 10), sharex=True, sharey="row"
         )
         im = ax1.pcolormesh(
             before_baseline_data.time,
             before_baseline_data.freq_chan,
             before_amp_stokesi.T,
             norm=norm,
+            cmap=cmap,
         )
         ax1.set(
             ylabel=f"Frequency / {before_baseline_data.freq_chan.unit:latex_inline}",
@@ -104,12 +106,14 @@ def plot_baseline_comparison_data(
             after_baseline_data.freq_chan,
             after_amp_stokesi.T,
             norm=norm,
+            cmap=cmap,
         )
         ax2.set(
             ylabel=f"Frequency / {after_baseline_data.freq_chan.unit:latex_inline}",
             title="After",
         )
-        fig.colorbar(im, ax=ax2, label="Stokes I Amplitude / Jy")
+        for ax in (ax1, ax2):
+            fig.colorbar(im, ax=ax, label="Stokes I Amplitude / Jy")
 
         # TODO: Move these delay calculations outside of the plotting function
         # And here we calculate the delay information
@@ -130,6 +134,7 @@ def plot_baseline_comparison_data(
             before_delays.delay,
             before_delays_i.T,
             norm=delay_norm,
+            cmap=cmap,
         )
         ax3.set(ylabel="Delay / s", title="Before")
         ax4.pcolormesh(
@@ -137,9 +142,11 @@ def plot_baseline_comparison_data(
             after_delays.delay,
             after_delays_i.T,
             norm=delay_norm,
+            cmap=cmap,
         )
         ax4.set(ylabel="Delay / s", title="After")
-        fig.colorbar(im, ax=ax4, label="Stokes I Amplitude / Jy")
+        for ax in (ax3, ax4):
+            fig.colorbar(im, ax=ax, label="Stokes I Amplitude / Jy")
 
         if w_delays is not None:
             for ax, baseline_data in zip(  # type:ignore[call-overload]
@@ -152,8 +159,8 @@ def plot_baseline_comparison_data(
                 ax.plot(
                     baseline_data.time,
                     w_delays.w_delays[b_idx],
-                    color="k",
-                    linestyle="--",
+                    color="tab:red",
+                    linestyle="-",
                     label=f"Delay for {w_delays.object_name}",
                 )
                 ax.legend()

{jolly_roger-0.2.0 → jolly_roger-0.3.0}/jolly_roger/tractor.py

@@ -202,17 +202,16 @@ def _get_data_chunk_from_main_table(
     logger.debug(f"Length of open table: {table_length} rows")
 
     lower_row = 0
-    upper_row = chunk_size
 
     while lower_row < table_length:
-        rows: list[dict[str, Any]] = ms_table[lower_row:upper_row]
-
-        data = _list_to_array(list_of_rows=rows, key=data_column)
-        flags = _list_to_array(list_of_rows=rows, key="FLAG")
-        uvws = _list_to_array(list_of_rows=rows, key="UVW")
-        time_centroid = _list_to_array(list_of_rows=rows, key="TIME_CENTROID")
-        ant_1 = _list_to_array(list_of_rows=rows, key="ANTENNA1")
-        ant_2 = _list_to_array(list_of_rows=rows, key="ANTENNA2")
+        data = ms_table.getcol(data_column, startrow=lower_row, nrow=chunk_size)
+        flags = ms_table.getcol("FLAG", startrow=lower_row, nrow=chunk_size)
+        uvws = ms_table.getcol("UVW", startrow=lower_row, nrow=chunk_size)
+        time_centroid = ms_table.getcol(
+            "TIME_CENTROID", startrow=lower_row, nrow=chunk_size
+        )
+        ant_1 = ms_table.getcol("ANTENNA1", startrow=lower_row, nrow=chunk_size)
+        ant_2 = ms_table.getcol("ANTENNA2", startrow=lower_row, nrow=chunk_size)
 
         yield DataChunkArray(
             data=data,
@@ -226,7 +225,6 @@ def _get_data_chunk_from_main_table(
         )
 
         lower_row += chunk_size
-        upper_row += chunk_size
 
 
 def get_data_chunks(
@@ -559,7 +557,8 @@ def _tukey_tractor(
         taper = 1.0 - taper
 
         # Delay with the elevation of the target object
-        elevation_mask = w_delays.elevation < (-3 * u.deg)
+        # TODO: Allow elevation to be a user parameter
+        elevation_mask = w_delays.elevation < tukey_tractor_options.elevation_cut
         taper[elevation_mask[time_idx], :, :] = 1.0
 
         # TODO: Handle case of aliased delays
@@ -619,6 +618,8 @@ class TukeyTractorOptions:
     """apply the taper using the delay towards the target object."""
     target_object: str = "Sun"
     """The target object to apply the delay towards."""
+    elevation_cut: u.Quantity = -1 * u.deg
+    """The elevation cut-off for the target object. Defaults to 0 degrees."""
 
 
 def tukey_tractor(