Merge branch 'main' into next

notebooks/__code/from_json_to_csv/main.py

@@ -0,0 +1,177 @@
+import numpy as np
+import os
+from IPython.core.display import HTML
+from ipywidgets import widgets
+from IPython.core.display import display
+
+from NeuNorm.normalization import Normalization
+
+from __code.ipywe import fileselector
+from __code.ipywe.myfileselector import FileSelectorPanelWithJumpFolders
+from __code import utilities, file_handler
+
+
+class FromJsonToCsv:
+
+    working_dir = ''
+    images_ui = None
+    data = []
+    list_file_names = []
+
+    def __init__(self, working_dir=''):
+        self.working_dir = working_dir
+        self.output_folder_ui = None
+
+    def select_images(self):
+        _instruction = 'Select files to convert'
+        self.images_ui = fileselector.FileSelectorPanel(instruction=_instruction,
+                                                        start_dir=self.working_dir,
+                                                        multiple=True,
+                                                        filters={"JSON": "*.json"},
+                                                        next=self.load)
+        self.images_ui.show()
+
+    def get_list_images(self):
+        return self.images_ui.selected
+
+    def load(self, list_json):
+        print(list_json)
+        # #list_images = self.get_list_images()
+        # self.list_file_names = list_images
+        # self.o_norm = Normalization()
+        # self.o_norm.load(file=list_images, notebook=True)
+        # self.data = self.o_norm.data['sample']['data']
+        # self.__calculate_image_dimension()
+
+    def __calculate_image_dimension(self):
+        _image_0 = self.data[0]
+        [self.image_dimension['height'], self.image_dimension['width']] = np.shape(_image_0)
+
+    def __bin_parameter_changed(self, sender):
+
+        new_width_bin = int(self.bin_width_para.value)
+        self.bin_width_value = new_width_bin
+
+        new_height_bin = int(self.bin_height_para.value)
+        self.bin_height_value = new_height_bin
+
+        old_width = self.image_dimension['width']
+        old_height = self.image_dimension['height']
+
+        new_width = int(old_width / new_width_bin)
+        new_height = int(old_height / new_height_bin)
+
+        self.right_widgets.children[1].value = "Width: {} pixels".format(new_width)
+        self.right_widgets.children[2].value = "Height: {} pixels".format(new_height)
+
+    def select_bin_parameter(self):
+        _width = self.image_dimension['width']
+        _height = self.image_dimension['height']
+        left_widgets = widgets.VBox([widgets.HTML(value="<b>Current Image Size:</b>",
+                                                  layout=widgets.Layout(width='250px')),
+                                     widgets.Label("Width: {} pixels".format(_width),
+                                                   layout=widgets.Layout(width='100%')),
+                                     widgets.Label("Height: {} pixels".format(_height),
+                                                   layout=widgets.Layout(width='100%'))])
+
+        options_list = [str(_) for _ in np.arange(2, 21)]
+        self.bin_width_para = widgets.Dropdown(options=options_list,
+                                               value='2',
+                                               description="width:",
+                                               continuous_update=False,
+                                               layout=widgets.Layout(width='80%'))
+        self.bin_width_para.observe(self.__bin_parameter_changed)
+
+        self.bin_height_para = widgets.Dropdown(options=options_list,
+                                                value='2',
+                                                description="height:",
+                                                continuous_update=False,
+                                                layout=widgets.Layout(width='80%'))
+        self.bin_height_para.observe(self.__bin_parameter_changed)
+
+        center_widgets = widgets.VBox([widgets.HTML("<b>Bin Parameter:</b>",
+                                                    layout=widgets.Layout(width='250px')),
+                                       self.bin_width_para,
+                                       self.bin_height_para])
+
+        self.right_widgets = widgets.VBox([widgets.HTML("<b>New Image Size:</b>",
+                                                   layout=widgets.Layout(width='250px')),
+                                      widgets.Label("Width: {} pixels".format(250),
+                                                    layout=widgets.Layout(width='100%')),
+                                      widgets.Label("Height: {} pixels".format(250),
+                                                    layout=widgets.Layout(width='100%'))])
+
+        self.__bin_parameter_changed(None)
+
+        full_widget = widgets.HBox([left_widgets,
+                                    center_widgets,
+                                    self.right_widgets])
+
+        display(full_widget)
+
+    def select_export_folder(self):
+        self.output_folder_ui = FileSelectorPanelWithJumpFolders(instruction='Select output folder...',
+                                                                 start_dir=self.working_dir,
+                                                                 multiple=False,
+                                                                 next=self.export,
+                                                                 type='directory',
+                                                                 show_jump_to_home=True,
+                                                                 show_jump_to_share=True)
+        # self.output_folder_ui.show()
+
+    def rebin_data(self, data=[]):
+        width_bin = self.bin_width_value
+        height_bin = self.bin_height_value
+
+        height = self.image_dimension['height']
+        width = self.image_dimension['width']
+
+        # checking if last bin size match other bins
+        new_height = height
+        _nbr_height_bin = int(np.floor(height / height_bin))
+        if not (np.mod(height, height_bin) == 0):
+            new_height = int(_nbr_height_bin * height_bin)
+        new_height = int(new_height)
+
+        new_width = width
+        _nbr_width_bin = int(np.floor(width / width_bin))
+        if not (np.mod(width, width_bin) == 0):
+            new_width = int(_nbr_width_bin * width_bin)
+        new_width = int(new_width)
+
+        _new_data = data[0: new_height, 0: new_width]
+        _new_data = _new_data.reshape(_nbr_height_bin, height_bin, _nbr_width_bin, width_bin)
+        data_rebinned = _new_data.mean(axis=3).mean(axis=1)
+
+        return data_rebinned
+
+    def get_input_folder(self):
+        list_files = self.list_file_names
+        _file0 = list_files[0]
+        full_dir_name = os.path.dirname(_file0)
+        return os.path.basename(full_dir_name)
+
+    def export(self, output_folder):
+
+        input_folder = self.get_input_folder()
+        # output_folder = os.path.abspath(os.path.join(self.output_folder_ui.selected,
+        #                                              "{}_rebin_by_{}".format(input_folder, self.bin_value)))
+        bin_string = f"{self.bin_height_value}height_{self.bin_width_value}width"
+        output_folder = os.path.abspath(os.path.join(output_folder, "{}_rebin_by_{}".format(input_folder, bin_string)))
+        utilities.make_dir(dir=output_folder, overwrite=False)
+
+        w = widgets.IntProgress()
+        w.max = len(self.list_file_names)
+        display(w)
+
+        for _index, _file in enumerate(self.list_file_names):
+            basename = os.path.basename(_file)
+            _base, _ext = os.path.splitext(basename)
+            output_file_name = os.path.join(output_folder, _base + '.tiff')
+            _rebin_data = self.rebin_data(self.data[_index])
+            file_handler.make_tiff(filename=output_file_name, data=_rebin_data)
+
+            w.value = _index + 1
+
+        display(HTML('<span style="font-size: 20px; color:blue">File created in ' + \
+                     output_folder + '</span>'))

notebooks/from_json_to_csv.ipynb

@@ -0,0 +1,33 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "849b2e13-92a6-4826-944f-080d5dae98d4",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.1"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}