Merge pull request #100 from HenriquesLab/checktypos

Check typos and output stability

Author: jdmartinez24

src/vlab4mic/analysis/_plots.py

@@ -14,7 +14,7 @@ def sns_heatmap_pivots(
     return_figure=False,
     metric_name=None,
     decimals="%.4f",
-    fillna = True,
+    na_as_zero = True,
     **kwargs,
 ):
     conditions = list(df_pivots.keys())
@@ -23,7 +23,7 @@ def sns_heatmap_pivots(
         annot_kws = {"size": 10, "rotation": 45}
     else:
         annot_kws = kwargs["annot_kws"]
-    f, axes = plt.subplots(nconditions, 2, figsize=figsize)
+    f, axes = plt.subplots(nconditions, 2, figsize=figsize, squeeze = False)
     plot_num = 0
     if cmaps_range == "same":
         # min and max here correspond to SSIM
@@ -37,7 +37,7 @@ def sns_heatmap_pivots(
     else:
         metric_n = "Metric"
     for n, cond in enumerate(conditions):
-        if fillna:
+        if na_as_zero:
             mask = df_pivots[cond][0].isna()
             df_pivots[cond][0][mask] = 0.0
             mask2 = df_pivots[cond][1].isna()

src/vlab4mic/analysis/sweep.py

@@ -840,7 +840,7 @@ def pivot_dataframes_byCategory(
             )
             .reset_index()
         )
-        # get mean and std accross parameter combinations of axes_param_names
+        # get mean and std across parameter combinations of axes_param_names
         condition_mean_pivot = summarised_group.pivot(
             index=param1, columns=param2, values="Mean_Value"
         ).round(4)

src/vlab4mic/generate/imaging.py

@@ -38,7 +38,7 @@ def __init__(self):
         self.field["reference_point"] = None
         self.fluorophore_params = (
             dict()
-        )  # contiain its photophysical parameters such as excitation and emission
+        )  # contain its photophysical parameters such as excitation and emission
         self.emitters_by_fluorophore = dict()
         self.emitters_by_channel = dict()
         self.writing_dir = ""
@@ -101,7 +101,7 @@ def _calculate_roi_ranges(self):
         ]
         self.roi_params["ranges"] = [xrange, yrange, zrange]
 
-    def get_absoulte_reference_point(self):
+    def get_absolute_reference_point(self):
         """
         Get the absolute reference point in 3D (including focus plane).
 
@@ -403,11 +403,11 @@ def _set_modality_channels(self, modality, fluorophores_in_channel, prints=False
                 if prints:
                     print(fluoname)
                 channel_name = "ch" + str(ch)
-                fluorophores_in_chanel = []
-                fluorophores_in_chanel.append(
+                fluorophores_in_channel = []
+                fluorophores_in_channel.append(
                     fluoname
                 )  # this is because a channel can have several fluorophores
-                filter_dictionary[channel_name] = fluorophores_in_chanel
+                filter_dictionary[channel_name] = fluorophores_in_channel
                 ch += 1
             self.modalities[modality]["filters"] = filter_dictionary
         else:
@@ -441,7 +441,7 @@ def _set_modality_psf(
         if "depth" not in self.modalities[modality]["psf"]:
             depth_default = int((psf_stack.shape)[2] / 2)
             if prints:
-                print("No depth parameter found for psf, asigning default")
+                print("No depth parameter found for psf, assigning default")
             self.modalities[modality]["psf"]["depth"] = depth_default
 
     def _set_modality_emission(self, modality, emission):
@@ -450,7 +450,7 @@ def _set_modality_emission(self, modality, emission):
     def _set_modality_detector(
         self,
         modality,
-        image_size=[],  # decpreciated, image size will only be taken from ROI
+        image_size=[],  # deprecated, image size will only be taken from ROI
         pixelsize=None,
         bits_pixel=None,
         noise_model=None,
@@ -480,7 +480,7 @@ def _set_modality_detector(
 
     def _calculate_imsize_from_ROIranges(
         self, mod_pixelsize
-    ):  # THere should be specified the scale of the pixelsize of modality
+    ):  # There should be specified the scale of the pixelsize of modality
         roi_scale = self.get_roi_params("scale")
         xrange = self.get_roi_params("ranges")[0]
         yrange = self.get_roi_params("ranges")[1]
@@ -585,7 +585,7 @@ def generate_imaging(
         **kwargs,
     ):
         """
-        Master funciton that generates image sequences depending on the modality
+        Master function that generates image sequences depending on the modality
         This function is responsible for
             Preparing the coordinates according to ROI (DONE!)
             Creating the Photons per frame matrix
@@ -609,7 +609,7 @@ def generate_imaging(
                 )
             else:
                 fluonames = list(self.modalities[modality]["filters"][ch])
-                # prepare a dictionary that conaints the emitters per channel defined
+                # prepare a dictionary that contains the emitters per channel defined
                 output_per_fluoname = dict()
                 writing_notes = self.identifier + "_" + str(modality) + "_" + str(ch) + "_"
                 for fluo in fluonames:  # a channel could capture multiple fluorophores
@@ -869,8 +869,8 @@ def add_detector_noise(self, modality, stack):
 
     def _adjust_to_pixel_depth(self, modality, stack):
         bits = self.modalities[modality]["detector"]["bits_pixel"]
-        saturaton = (2**bits) - 1
-        stack[stack > saturaton] == saturaton
+        saturation = (2**bits) - 1
+        stack[stack > saturation] == saturation
         return stack
 
     def _save_timeseries_with_beads(self, timeseries_stack, beads_stack, notes):
@@ -1212,7 +1212,7 @@ def show_field(
         ax.plot_surface(xx, yy, zz, alpha=0.2)
         # show ROI reference point
         if reference_pt:
-            ref_pt = self.get_absoulte_reference_point() * factor
+            ref_pt = self.get_absolute_reference_point() * factor
             add_ax_scatter(ax, format_coordinates(ref_pt))
         # EMITTERS PER FLUOROPHORE SPECIES
         if self.emitters_by_fluorophore is not None:

src/vlab4mic/generate/molecular_structure.py

@@ -597,7 +597,7 @@ def gen_targets_by_sequence(self, target_name, sequence, **kwargs):
         **kwargs
             Additional keyword arguments (e.g., fluorophore, labeling_efficiency, method).
         """
-        #  only the first appearance of the epitope in every chain is retreived
+        #  only the first appearance of the epitope in every chain is retrieved
         #  if a chain has more than one epitope, only the first one is returned
         target_seq = sequence
         method = "average"

src/vlab4mic/sweep_generator.py

@@ -95,6 +95,8 @@ def __init__(self):
         self.plot_parameters["lineplots"]["style"] = None
         self.plot_parameters["lineplots"]["estimator"] = "mean"
         self.plot_parameters["lineplots"]["errorbar"] = "ci"
+        self.plot_parameters["general"] = {}
+        self.plot_parameters["general"]["na_as_zero"] = True
         self.structures_info_list = self.experiment.structures_info_list
         # Use the directly loaded parameter_settings instead of experiment.param_settings
         # to ensure all parameter groups (including particle_defect) are available
@@ -753,6 +755,22 @@ def set_plot_parameters(self, plot_type, **kwargs):
             for key, val in kwargs.items():
                 self.plot_parameters[plot_type][key] = val
 
+    def set_na_as_zero_in_plots(self, na_as_zero: bool = True):
+        """
+        Set whether to treat NaN values as zero in plots.
+
+        Parameters
+        ----------
+        :param na_as_zero: bool, optional
+            If True, NaN values will be treated as zero in plots. Defaults to True.
+            This does not affect the underlying data, only the visualization.
+
+        Returns
+        -------
+        None
+        """
+        self.plot_parameters["general"]["na_as_zero"] = na_as_zero        
+
     def run_analysis(
         self,
         save=True,
@@ -818,6 +836,7 @@ def run_analysis(
                         return_figure=True,
                         metric_name=metric_name,
                         filter_dictionary=None,
+                        na_as_zero=self.plot_parameters["general"]["na_as_zero"],
                     )
         if save:
             self.save_analysis(
@@ -876,6 +895,7 @@ def generate_analysis_plots(
         decimals: int = None,
         return_figure=True,
         filter_dictionary=None,
+        na_as_zero = True,
         **kwargs,
     ):
         """
@@ -918,6 +938,7 @@ def generate_analysis_plots(
                 return_figure=return_figure,
                 decimals=decimals,
                 filter_dictionary=filter_dictionary,
+                na_as_zero = na_as_zero,
                 **plot_params,
                 **kwargs
             )
@@ -929,6 +950,7 @@ def generate_analysis_plots(
                 decimals=decimals,
                 return_figure=return_figure,
                 filter_dictionary=filter_dictionary,
+                na_as_zero = na_as_zero,
                 **plot_params,
                 **kwargs
             )
@@ -945,6 +967,7 @@ def _gen_heatmaps(
         filter_dictionary=None,
         annotations=False,
         palette=None,
+        na_as_zero = False,
         **kwargs,
     ):
         """
@@ -1016,6 +1039,7 @@ def _gen_heatmaps(
             metric_name=metric_name,
             conditions_cmaps=[cmap_palette]*nconditions,
             decimals=decimals,
+            na_as_zero = na_as_zero,
             **kwargs
         )
         return plot
@@ -1034,6 +1058,7 @@ def _gen_lineplots(
         decimals="%.4f",
         return_figure=True,
         filter_dictionary=None,
+        na_as_zero = False,
         **kwargs,
     ):
         """
@@ -1079,8 +1104,13 @@ def _gen_lineplots(
         if style is None and len(self.parameters_with_set_values) > 1:
             style = self.parameters_with_set_values[1]
         fig, axes = plt.subplots(figsize=figsize)
+        if na_as_zero:
+            data_to_plot = data.copy(deep=True)
+            data_to_plot.fillna(0, inplace=True)
+        else:
+            data_to_plot = data
         sns.lineplot(
-            data=data,
+            data=data_to_plot,
             x=x_param,
             y=metric_name,
             hue=hue,
@@ -1095,7 +1125,7 @@ def _gen_lineplots(
         axes.xaxis.set_major_formatter(FormatStrFormatter(decimals))
         title = estimator + " " + metric_name + " for " + x_param
         if style is not None:
-            title = title + "per " + style
+            title = title + " per " + style
         plt.title(title)
         plt.close()
         return fig
@@ -1140,6 +1170,17 @@ def save_analysis(
             if keyname == "dataframes":
                 df = self.get_analysis_output(keyname)
                 df_name = output_name + "_dataframe.csv"
+                files_indir = os.listdir(output_directory)
+                if df_name in files_indir:
+                    count = 1
+                    df_name = (
+                        output_name + "_dataframe_" + str(count) + ".csv"
+                    )
+                    while df_name in files_indir:
+                        count += 1
+                        df_name = (
+                            output_name + "_dataframe_" + str(count) + ".csv"
+                        )
                 df.to_csv(os.path.join(output_directory, df_name), index=False)
             elif keyname == "plots":
                 plots_dictionary = self.get_analysis_output(keyname)
@@ -1153,6 +1194,31 @@ def save_analysis(
                             + plot_type
                             + ".png"
                         )
+                        current_files = os.listdir(output_directory)
+                        if figure_name in current_files:
+                            count = 1
+                            figure_name = (
+                                output_name
+                                + "_"
+                                + metric
+                                + "_"
+                                + plot_type
+                                + "_"
+                                + str(count)
+                                + ".png"
+                            )
+                            while figure_name in current_files:
+                                dt_string = dt_string + "_1"
+                                figure_name = (
+                                    output_name
+                                    + "_"
+                                    + metric
+                                    + "_"
+                                    + plot_type
+                                    + "_"
+                                    + str(count)
+                                    + ".png"
+                                )
                         plot.savefig(
                             os.path.join(output_directory, figure_name)
                         )
@@ -1182,11 +1248,21 @@ def save_images(self, output_name=None, output_directory=None, floats_as=float):
         - If `self.reference_image` is present, saves it as "reference.tiff" in the output directory.
         - Saves acquisition parameters as a YAML file in the output directory.
         """
+        now = datetime.now()  # dd/mm/YY H:M:S
+        dt_string = now.strftime("%Y%m%d")
         if output_name is None:
             output_name = "vLab4mic_images_"
         if output_directory is None:
+            foldername = "simulated_images_" + dt_string
+            filesindir = os.listdir(self.output_directory)
+            if foldername in filesindir:
+                count = 1
+                foldername = "simulated_images_" + dt_string + "_" + str(count)
+                while foldername in filesindir:
+                    count+=1
+                    foldername = "simulated_images_" + dt_string + "_" + str(count)
             output_directory = os.path.join(
-                self.output_directory, "simulated_images", ""
+                self.output_directory, foldername
             )
             if not os.path.exists(output_directory):
                 os.makedirs(output_directory)
@@ -1198,8 +1274,9 @@ def save_images(self, output_name=None, output_directory=None, floats_as=float):
             image = replicates[0]
             for i in range(1, nreps):
                 image = np.concatenate((image, replicates[i]))
-            name = output_directory + param_combination_id + ".tiff"
-            tiff.imwrite(name, image)
+            name = param_combination_id + ".tiff"
+            dir_name = os.path.join(output_directory, name)
+            tiff.imwrite(dir_name, image)
         if floats_as is not None and callable(floats_as):
             copy_of_params = copy.deepcopy(self.acquisition_outputs_parameters)
             for combination_id, list_of_parameters in copy_of_params.items():
@@ -1221,8 +1298,10 @@ def save_images(self, output_name=None, output_directory=None, floats_as=float):
             )
         if self.reference_image is not None:
             # save reference image
-            name_ref = output_directory + "reference.tiff"
-            tiff.imwrite(name_ref, self.reference_image)
+            name_ref = param_combination_id + ".tiff"
+            dir_name_ref = os.path.join(output_directory, name_ref)
+            #name_ref = output_directory + "reference.tiff"
+            tiff.imwrite(dir_name_ref, self.reference_image)
 
 
 def run_parameter_sweep(
@@ -1271,6 +1350,8 @@ def run_parameter_sweep(
     psf_voxel_nm = None,
     depth_of_field_nm = None,
     exp_time = None,
+    # for plot generation
+    na_as_zero = True,
     # Add more as needed for your sweep
 ):
     """
@@ -1369,7 +1450,7 @@ def run_parameter_sweep(
     sweep_gen.select_modalities(modalities=modalities)
     sweep_gen.set_output_directory(output_directory=output_directory)
     sweep_gen.set_number_of_repetitions(sweep_repetitions)
-    # number of particles accross sweep
+    # number of particles across sweep
     if particle_positions is not None:
         # set those positions
         sweep_gen.experiment.set_virtualsample_params(
@@ -1416,6 +1497,7 @@ def run_parameter_sweep(
         reference_structure=reference_structure,
         reference_probe=reference_probe,
         **reference_parameters)
+    sweep_gen.set_na_as_zero_in_plots(na_as_zero=na_as_zero)
     if run_analysis:
         sweep_gen.run_analysis(
             save=save_analysis_results, 

src/vlab4mic/utils/data_format/configuration_format.py

@@ -79,11 +79,11 @@ def compile_modality_parameters(
                 if prints:
                     print(fluoname)
                 channel_name = "ch" + str(ch)
-                fluorophores_in_chanel = []
-                fluorophores_in_chanel.append(
+                fluorophores_in_channel = []
+                fluorophores_in_channel.append(
                     fluoname
                 )  # this is because a channel can have several fluorophores
-                filter_dictionary[channel_name] = fluorophores_in_chanel
+                filter_dictionary[channel_name] = fluorophores_in_channel
                 ch += 1
         else:
             filter_dictionary = mod_pars["filters"]