cloudnetpy 1.56.5__py3-none-any.whl → 1.56.6__py3-none-any.whl

cloudnetpy/exceptions.py

@@ -23,6 +23,13 @@ class RadarDataError(CloudnetException):
         super().__init__(msg)
 
 
+class PlottingError(CloudnetException):
+    """Internal exception class."""
+
+    def __init__(self, msg: str):
+        super().__init__(msg)
+
+
 class WeatherStationDataError(CloudnetException):
     """Internal exception class."""
 

cloudnetpy/plotting/plotting.py

@@ -16,6 +16,7 @@ from matplotlib.transforms import Affine2D, Bbox
 from mpl_toolkits.axes_grid1 import make_axes_locatable
 from numpy import ma, ndarray
 
+from cloudnetpy.exceptions import PlottingError
 from cloudnetpy.plotting.plot_meta import ATTRIBUTES, PlotMeta
 
 
@@ -129,7 +130,7 @@ class FigureData:
                 variable_indices.append(extracted_ind)
         if not valid_variables:
             msg = f"None of the variables {requested_variables} found in the file."
-            raise ValueError(msg)
+            raise PlottingError(msg)
         return valid_variables, variable_indices
 
     def _get_height(self) -> np.ndarray | None:
@@ -270,8 +271,10 @@ class Plot:
         )
         if conversion_method == multiply:
             self._data *= conversion
+            self._data_orig *= conversion
         elif conversion_method == add:
             self._data += conversion
+            self._data_orig += conversion
         if units is not None:
             return units
         units = getattr(self.sub_plot.variable, "units", "")
@@ -309,7 +312,7 @@ class Plot:
         max_gap_fraction_hour = _get_max_gap_in_minutes(figure_data) / 60
 
         if figure_data.file.cloudnet_file_type == "model":
-            time, data = self._get_unmasked_model_values(time, data)
+            time, data = screen_completely_masked_profiles(time, data)
 
         gap_indices = np.where(np.diff(time) > max_gap_fraction_hour)[0]
         if not ma.is_masked(data):
@@ -348,21 +351,16 @@ class Plot:
         self._data = data_new
         figure_data.time_including_gaps = time_new
 
-    @staticmethod
-    def _get_unmasked_model_values(time: np.ndarray, data: ma.MaskedArray) -> tuple:
-        good_ind = np.where(np.any(~data.mask, axis=1))[0]
-        if len(good_ind) == 0:
-            msg = "No unmasked values in the file."
-            raise ValueError(msg)
-        good_ind = np.append(good_ind, good_ind[-1] + 1)
-        good_ind = np.clip(good_ind, 0, len(time) - 1)
-        return time[good_ind], data[good_ind, :]
-
-    def _read_flags(self, figure_data: FigureData) -> np.ndarray:
-        flag_name = f"{self.sub_plot.variable.name}_quality_flag"
-        if flag_name not in figure_data.variables:
-            flag_name = "temperature_quality_flag"
-        return figure_data.file.variables[flag_name][:] > 0
+    def _read_flagged_data(self, figure_data: FigureData) -> np.ndarray:
+        flag_names = [
+            f"{self.sub_plot.variable.name}_quality_flag",
+            "temperature_quality_flag",
+            "quality_flag",
+        ]
+        for flag_name in flag_names:
+            if flag_name in figure_data.file.variables:
+                return figure_data.file.variables[flag_name][:] > 0
+        return np.array([])
 
 
 class Plot2D(Plot):
@@ -385,7 +383,7 @@ class Plot2D(Plot):
             self._fill_flagged_data(figure_data)
 
     def _fill_flagged_data(self, figure_data: FigureData) -> None:
-        flags = self._read_flags(figure_data)
+        flags = self._read_flagged_data(figure_data)
         batches = find_batches_of_ones(flags)
         for batch in batches:
             if batch[0] == batch[1]:
@@ -394,10 +392,9 @@ class Plot2D(Plot):
             self._ax.fill_between(
                 time_batch,
                 *self._get_y_limits(),
-                facecolor="mistyrose",
-                alpha=1,
-                hatch=r"\\",
-                edgecolor="lightsalmon",
+                facecolor="whitesmoke",
+                alpha=0.7,
+                edgecolor="grey",
                 label="_nolegend_",
             )
 
@@ -469,12 +466,18 @@ class Plot2D(Plot):
 
 
 class Plot1D(Plot):
-    def plot_tb(self, figure_data: FigureData, ind: int):
-        flagged_data = self._pointing_filter(figure_data, ind)
-        self.plot(figure_data)
-        if ma.count(flagged_data) > 0:
-            self.plot_flag_data(figure_data.time, flagged_data)
+    def plot_tb(self, figure_data: FigureData, freq_ind: int):
+        self._data = self._data[:, freq_ind]
+        self._data_orig = self._data_orig[:, freq_ind]
+        is_bad_zenith = self._get_bad_zenith_profiles(figure_data)
+        self._data[is_bad_zenith] = ma.masked
+        self._data_orig[is_bad_zenith] = ma.masked
+        flags = self._read_flagged_data(figure_data)[:, freq_ind]
+        flags[is_bad_zenith] = False
+        if np.any(flags):
+            self.plot_flag_data(figure_data.time[flags], self._data_orig[flags])
             self.add_legend()
+        self.plot(figure_data)
 
     def plot_flag_data(self, time: np.ndarray, values: np.ndarray) -> None:
         self._ax.plot(
@@ -511,7 +514,7 @@ class Plot1D(Plot):
         pos = self._ax.get_position()
         self._ax.set_position((pos.x0, pos.y0, pos.width * 0.965, pos.height))
         if figure_data.is_mwrpy_product():
-            flags = self._read_flags(figure_data)
+            flags = self._read_flagged_data(figure_data)
             if np.any(flags):
                 self.plot_flag_data(figure_data.time[flags], self._data_orig[flags])
                 self.add_legend()
@@ -556,8 +559,9 @@ class Plot1D(Plot):
         return min(max(line_width, 0.25), 0.9)
 
     def _plot_moving_average(self, figure_data: FigureData):
-        time = figure_data.time_including_gaps.copy()
-        data, time = self._get_unmasked_values(self._data, time)
+        time = figure_data.time.copy()
+        data = self._data_orig.copy()
+        data, time = self._get_unmasked_values(data, time)
         sma = self._calculate_moving_average(data, time, window=5)
         gap_time = _get_max_gap_in_minutes(figure_data)
         gaps = self._find_time_gap_indices(time, max_gap_min=gap_time)
@@ -574,24 +578,17 @@ class Plot1D(Plot):
         good_values = ~data.mask
         return data[good_values], time[good_values]
 
-    def _pointing_filter(self, figure_data: FigureData, ind: int) -> ndarray:
+    @staticmethod
+    def _get_bad_zenith_profiles(figure_data: FigureData) -> np.ndarray:
         zenith_limit = 5
-        status = 0
-        self._data = self._data[:, ind]
-        flagged_data = ma.masked_all_like(figure_data.time)
+        valid_pointing_status = 0
         if "pointing_flag" in figure_data.file.variables:
             pointing_flag = figure_data.file.variables["pointing_flag"][:]
             zenith_angle = figure_data.file.variables["zenith_angle"][:]
-            quality_flag = figure_data.file.variables["quality_flag"][:, ind]
-            # First mask bad zenith angle points
-            self._data[np.abs(zenith_angle) > zenith_limit] = ma.masked
-            self._data[pointing_flag != status] = ma.masked
-            # Store flagged data points for visualization
-            valid_ind = np.where(quality_flag != status)[0]
-            if len(valid_ind) > 0:
-                flagged_data[valid_ind] = self._data[valid_ind]
-            self._data[quality_flag != status] = ma.masked
-        return flagged_data
+            is_bad_zenith = np.abs(zenith_angle) > zenith_limit
+            is_bad_pointing = pointing_flag != valid_pointing_status
+            return is_bad_zenith | is_bad_pointing
+        return np.zeros_like(figure_data.time, dtype=bool)
 
     @staticmethod
     def _find_time_gap_indices(time: ndarray, max_gap_min: float) -> ndarray:
@@ -750,3 +747,15 @@ def find_batches_of_ones(array: np.ndarray) -> list[tuple[int, int]]:
     starts = np.where(np.diff(np.hstack(([0], array))) == 1)[0]
     stops = np.where(np.diff(np.hstack((array, [0]))) == -1)[0]
     return list(zip(starts, stops, strict=True))
+
+
+def screen_completely_masked_profiles(time: np.ndarray, data: ma.MaskedArray) -> tuple:
+    if not ma.is_masked(data):
+        return time, data
+    good_ind = np.where(np.any(~data.mask, axis=1))[0]
+    if len(good_ind) == 0:
+        msg = "All values masked in the file."
+        raise PlottingError(msg)
+    good_ind = np.append(good_ind, good_ind[-1] + 1)
+    good_ind = np.clip(good_ind, 0, len(time) - 1)
+    return time[good_ind], data[good_ind, :]

cloudnetpy/version.py

@@ -1,4 +1,4 @@
 MAJOR = 1
 MINOR = 56
-PATCH = 5
+PATCH = 6
 __version__ = f"{MAJOR}.{MINOR}.{PATCH}"

{cloudnetpy-1.56.5.dist-info → cloudnetpy-1.56.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cloudnetpy
-Version: 1.56.5
+Version: 1.56.6
 Summary: Python package for Cloudnet processing
 Author: Simo Tukiainen
 License: MIT License

{cloudnetpy-1.56.5.dist-info → cloudnetpy-1.56.6.dist-info}/RECORD

@@ -3,12 +3,12 @@ cloudnetpy/cloudnetarray.py,sha256=vSI6hqozhS1ntNIgY2kqTt7N6BF_xJtUii_vsuyxTno,6
 cloudnetpy/concat_lib.py,sha256=YK5ho5msqwNxpPtPT8f2OewIJ8hTrbhCkaxHaBKLTI0,9809
 cloudnetpy/constants.py,sha256=OMp3pKHCZmdKyRvfO35E7vE3FrS_DHIs_GJuexJLCQk,600
 cloudnetpy/datasource.py,sha256=-6oLC5bsn9sIoaN0glV88owFyTeGRsW1ZVJSV8rM5rE,7813
-cloudnetpy/exceptions.py,sha256=NsuB5gTA8NvpmxykIJjHOWObTPpAerzpofs8xrFA1ow,1272
+cloudnetpy/exceptions.py,sha256=nA6YieylwKSp5KQOh3DhhcTmUBsd0tBZnedgmlWck-w,1415
 cloudnetpy/metadata.py,sha256=Bcu1a9UyUq61jomuZ0_6hYIOzf61e5qCXeiwLm46ikw,5040
 cloudnetpy/output.py,sha256=jD1pfBb4OQhVOrlhPEk-8FAi4bUW7zjAL468r6BPkJg,14586
 cloudnetpy/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cloudnetpy/utils.py,sha256=yY5a5HLuAks2uzA4XbbqsGFEmXoyqECn_TjD3sMa0lI,27193
-cloudnetpy/version.py,sha256=6cv25AS5sFm-DzOvNw4RB7-2flKWgFkjLMkIKHBnLD0,72
+cloudnetpy/version.py,sha256=KcLO5w70O8aXSbgK5nqMVq2YM5wAvubh8Uf9D1Q4FNc,72
 cloudnetpy/categorize/__init__.py,sha256=gP5q3Vis1y9u9OWgA_idlbjfWXYN_S0IBSWdwBhL_uU,69
 cloudnetpy/categorize/atmos.py,sha256=cax3iRmvr7S-VkUZqz0JCfAN3WEsUVbGfH4zSHy1APo,12384
 cloudnetpy/categorize/atmos_utils.py,sha256=wndpwJxc2-QnNTkV8tc8I11Vs_WkNz9sVMX1fuGgUC4,3777
@@ -92,7 +92,7 @@ cloudnetpy/model_evaluation/tests/unit/test_statistical_methods.py,sha256=Ra3r4V
 cloudnetpy/model_evaluation/tests/unit/test_tools.py,sha256=Ia_VrLdV2NstX5gbx_3AZTOAlrgLAy_xFZ8fHYVX0xI,3817
 cloudnetpy/plotting/__init__.py,sha256=2-8x8d1AfAhfU15RwWhusD0Wot_g6Ob_jJoywbrTC7A,95
 cloudnetpy/plotting/plot_meta.py,sha256=xbiEU9Okx5L_WG7KtVnljxjpCYcgqyOLywBc49gibSQ,13033
-cloudnetpy/plotting/plotting.py,sha256=jUn64USNApkL_c6FXAr30hW2Xc_M8WZthqVgjuCgN0M,26667
+cloudnetpy/plotting/plotting.py,sha256=NjeWF5u7fSvNVCwvOu8RyxQ7bApm7K74CF4I2sDCR40,26868
 cloudnetpy/products/__init__.py,sha256=2hRb5HG9hNrxH1if5laJkLeFeaZCd5W1q3hh4ewsX0E,273
 cloudnetpy/products/classification.py,sha256=J_FOMUSyxvFaT-hvdKVVcKPtuQ0u3V9PsV5xaIKzMjg,7843
 cloudnetpy/products/der.py,sha256=HAdPvbJySEqkIwDrdZDPnli_wnN2qwm72_D1a82ZWIs,12398
@@ -106,8 +106,8 @@ cloudnetpy/products/mie_lu_tables.nc,sha256=It4fYpqJXlqOgL8jeZ-PxGzP08PMrELIDVe5
 cloudnetpy/products/mwr_tools.py,sha256=TsVEqNwzoDv90TgzUSnJjMuc3C1KQ-hwsIZ8t0IdDJ4,4407
 cloudnetpy/products/product_tools.py,sha256=E8CSijBY8cr70BH2JFa0lGQ-RzI9EcHQ0Fzt8CQ8rY4,10442
 docs/source/conf.py,sha256=IKiFWw6xhUd8NrCg0q7l596Ck1d61XWeVjIFHVSG9Og,1490
-cloudnetpy-1.56.5.dist-info/LICENSE,sha256=wcZF72bdaoG9XugpyE95Juo7lBQOwLuTKBOhhtANZMM,1094
-cloudnetpy-1.56.5.dist-info/METADATA,sha256=x8u7BhZ4EiuxFV80zTN-LaHuqkAU8TKlOMLR0FAzCHo,5733
-cloudnetpy-1.56.5.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-cloudnetpy-1.56.5.dist-info/top_level.txt,sha256=ibSPWRr6ojS1i11rtBFz2_gkIe68mggj7aeswYfaOo0,16
-cloudnetpy-1.56.5.dist-info/RECORD,,
+cloudnetpy-1.56.6.dist-info/LICENSE,sha256=wcZF72bdaoG9XugpyE95Juo7lBQOwLuTKBOhhtANZMM,1094
+cloudnetpy-1.56.6.dist-info/METADATA,sha256=kr-kst-d8xZSZA6N5IpUhsoRdab_rPEEXAmWlPS1pXo,5733
+cloudnetpy-1.56.6.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+cloudnetpy-1.56.6.dist-info/top_level.txt,sha256=ibSPWRr6ojS1i11rtBFz2_gkIe68mggj7aeswYfaOo0,16
+cloudnetpy-1.56.6.dist-info/RECORD,,