Merge remote-tracking branch 'origin/main'

doc/README.md

@@ -1727,7 +1727,7 @@ The script can be executed directly using the executable file: <code><a href="ht
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-&#8226 File management: For loop procedure, in the initial phase, the algorithm ingests the <code>best_nanoloops</code> directory along with the <code>properties</code> directory, and the property folder contains the <code>parameters.txt</code> file generated after steps 1 and 2 of the analysis. For curve procedure, the algorithm extract raw SSPFM file measurements and the property folder contains the <a href="https://github.com/CEA-MetroCarac/PySSPFM/blob/main/resources/measurement%20sheet%20model%20SSPFM.csv">measurement sheet model SSPFM</a> file <code>measurement_sheet_parameters.csv</code>.<br>
+&#8226 File management: For loop procedure, in the initial phase, the algorithm ingests the <code>best_nanoloops</code> directory along with the <code>properties</code> directory, and the property folder contains the parameters of json file of 2nd step of analysis. For curve procedure, the algorithm extract raw SSPFM file measurements and the property folder contains the <a href="https://github.com/CEA-MetroCarac/PySSPFM/blob/main/resources/measurement%20sheet%20model%20SSPFM.csv">measurement sheet model SSPFM</a> file <code>measurement_sheet_parameters.csv</code>.<br>
 &#8226 Common (user) parameters: all parameters common to the entire (both loop or curve) clustering analysis. Two distinct clustering algorithms exist: one for loops and the other for curves, specified with the <code>object</code> parameter.<br>
 &#8226 Loop parameters: all parameters common to the analysis of a clustering associated with a loop (best nanoloops generated after the second processing step). <br>
 &#8226 Curve parameters: all parameters common to the analysis of a clustering associated with a curve (raw SSPFM measurement channels). <br>
@@ -1835,7 +1835,7 @@ The script can be executed directly using the executable file: <code><a href="ht
 ```
 
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-&#8226 File management: For input, the algorithm requires the directory generated after the second processing step (see section <a href="https://github.com/CEA-MetroCarac/PySSPFM/tree/main/doc#vi---second-step-of-data-analysis">VI) - Second step of data analysis</a> of the documentation). It can be supplemented with the respective folders: <code>properties</code> for material properties, <code>nanoloops</code> containing measurements in the form of nanoloops (generated after the first processing step (see section <a href="https://github.com/CEA-MetroCarac/PySSPFM/tree/main/doc#iv---first-step-of-data-analysis">IV) - First step of data analysis</a> of the documentation)), and the text file containing measurement and processing parameters, <code>parameters.txt</code>.<br>
+&#8226 File management: For input, the algorithm requires the directory generated after the second processing step (see section <a href="https://github.com/CEA-MetroCarac/PySSPFM/tree/main/doc#vi---second-step-of-data-analysis">VI) - Second step of data analysis</a> of the documentation). It can be supplemented with the respective folders: <code>properties</code> for material properties, <code>nanoloops</code> containing measurements in the form of nanoloops (generated after the first processing step (see section <a href="https://github.com/CEA-MetroCarac/PySSPFM/tree/main/doc#iv---first-step-of-data-analysis">IV) - First step of data analysis</a> of the documentation)), and the csv measurement sheet containing measurement parameters.<br>
 &#8226 Mode: Choose from <code>'off'</code>, <code>'on'</code>, or <code>'coupled'.</code><br>
 &#8226 Mask parameters<br>
 &#8226 Hysteresis treatment parameters: Utilized for fitting the mean hysteresis.<br>
@@ -1864,7 +1864,7 @@ The data of the measured properties (generated after the second processing step
 #### VIII.5.c) Find best loop
 
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-Subsequently, for each of the selected measurement points, the finest among the loops is to be extracted with the aid of the <code>find_best_loops</code> function. This function acquires the measurement parameters from the <code>parameters.txt</code> file and invokes the <code>single_script</code> function found in <code><a href="https://github.com/CEA-MetroCarac/PySSPFM/blob/main/PySSPFM/data_processing/nanoloop_to_hyst_s2.py">data_processing/nanoloop_to_hyst_s2.py</a></code> to retrieve data from the <code>nanoloops</code> files and determine the optimum loop, referred to as the <code>best_loop</code>. In the case of a coupled measurement (<code>mode = 'coupled'</code>), this protocol is repeated for the on and off field modes. If the setting <code>electrostatic_offset is True</code>, the offsets in the <code>'off field'</code> mode are utilized to reconstruct the entirety of the electrostatic component (accounting for the CPD) (section <a href="https://github.com/CEA-MetroCarac/PySSPFM/tree/main/doc#vi4d---differential-analysis-of-on-and-off-field-hysteresis">VI.4.d) - Differential analysis of on and off field hysteresis</a> in the documentation).
+Subsequently, for each of the selected measurement points, the finest among the loops is to be extracted with the aid of the <code>find_best_loops</code> function. This function acquires the measurement parameters from the csv measurement sheet and invokes the <code>single_script</code> function found in <code><a href="https://github.com/CEA-MetroCarac/PySSPFM/blob/main/PySSPFM/data_processing/nanoloop_to_hyst_s2.py">data_processing/nanoloop_to_hyst_s2.py</a></code> to retrieve data from the <code>nanoloops</code> files and determine the optimum loop, referred to as the <code>best_loop</code>. In the case of a coupled measurement (<code>mode = 'coupled'</code>), this protocol is repeated for the on and off field modes. If the setting <code>electrostatic_offset is True</code>, the offsets in the <code>'off field'</code> mode are utilized to reconstruct the entirety of the electrostatic component (accounting for the CPD) (section <a href="https://github.com/CEA-MetroCarac/PySSPFM/tree/main/doc#vi4d---differential-analysis-of-on-and-off-field-hysteresis">VI.4.d) - Differential analysis of on and off field hysteresis</a> in the documentation).
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@@ -1922,7 +1922,7 @@ $$ R_{ij} = {c_{ij} \over \sqrt{c_{ii} * c_{jj}}} $$
 ```
 
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-&#8226 File management: For input, the algorithm requires the directory generated after the second processing step (see section <a href="https://github.com/CEA-MetroCarac/PySSPFM/tree/main/doc#vi---second-step-of-data-analysis">VI) - Second step of data analysis</a> of the documentation). It can be supplemented with the respective folders: <code>properties</code> for material properties, <code>nanoloops</code> containing measurements in the form of nanoloops (generated after the first processing step (see section <a href="https://github.com/CEA-MetroCarac/PySSPFM/tree/main/doc#iv---first-step-of-data-analysis">IV) - First step of data analysis</a> of the documentation)), and the text file containing measurement and processing parameters, <code>parameters.txt</code>.<br>
+&#8226 File management: For input, the algorithm requires the directory generated after the second processing step (see section <a href="https://github.com/CEA-MetroCarac/PySSPFM/tree/main/doc#vi---second-step-of-data-analysis">VI) - Second step of data analysis</a> of the documentation). It can be supplemented with the respective folders: <code>properties</code> for material properties, <code>nanoloops</code> containing measurements in the form of nanoloops (generated after the first processing step (see section <a href="https://github.com/CEA-MetroCarac/PySSPFM/tree/main/doc#iv---first-step-of-data-analysis">IV) - First step of data analysis</a> of the documentation)), and the csv measurement sheet containing measurement parameters.<br>
 &#8226 Measurement selection parameters<br>
 &#8226 Mask parameters<br>
 &#8226 Save and plot parameters: Pertaining to the management of display and the preservation of results. <br>
@@ -1995,7 +1995,7 @@ The script can be executed directly using the executable file: <code><a href="ht
 ```
 
 <p align="justify" width="100%">
-&#8226 File management: For input, the algorithm requires the directory generated after the second processing step (see section <a href="https://github.com/CEA-MetroCarac/PySSPFM/tree/main/doc#vi---second-step-of-data-analysis">VI) - Second step of data analysis</a> of the documentation). It can be supplemented with the respective folders: <code>properties</code> for material properties, <code>nanoloops</code> containing measurements in the form of nanoloops (generated after the first processing step (see section <a href="https://github.com/CEA-MetroCarac/PySSPFM/tree/main/doc#iv---first-step-of-data-analysis">IV) - First step of data analysis</a> of the documentation)), and the text file containing measurement and processing parameters, <code>parameters.txt</code>.<br>
+&#8226 File management: For input, the algorithm requires the directory generated after the second processing step (see section <a href="https://github.com/CEA-MetroCarac/PySSPFM/tree/main/doc#vi---second-step-of-data-analysis">VI) - Second step of data analysis</a> of the documentation). It can be supplemented with the respective folders: <code>properties</code> for material properties, <code>nanoloops</code> containing measurements in the form of nanoloops (generated after the first processing step (see section <a href="https://github.com/CEA-MetroCarac/PySSPFM/tree/main/doc#iv---first-step-of-data-analysis">IV) - First step of data analysis</a> of the documentation)), and the csv measurement sheet containing measurement parameters.<br>
 &#8226 Measurement selection parameters<br>
 &#8226 Pixel selection parameters<br>
 &#8226 Loop plotting parameter (<code>del_first_loop</code>)<br>
@@ -2016,7 +2016,7 @@ The script can be executed directly using the executable file: <code><a href="ht
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-The initial step entails the extraction of properties generated after the second processing step (see section <a href="https://github.com/CEA-MetroCarac/PySSPFM/tree/main/doc#vi---second-step-of-data-analysis">VI) - Second step of data analysis</a> of the documentation), residing within the folder <code>properties</code>, accomplished by the <code>extract_properties</code> function in the script <code><a href="https://github.com/CEA-MetroCarac/PySSPFM/blob/main/PySSPFM/utils/nanoloop_to_hyst/file.py">utils/nanoloop_to_hyst/file.py</a></code>. The property selected by the user through the <code>'meas key'</code> parameter, serving as a sorting reference, is then singled out among all others. The extraction of processing and measurement parameters from the file <code>parameters.txt</code> is carried out using the <code>extract_params</code> function from the script. The measurement files are then sorted under two scenarios: <br>
+The initial step entails the extraction of properties generated after the second processing step (see section <a href="https://github.com/CEA-MetroCarac/PySSPFM/tree/main/doc#vi---second-step-of-data-analysis">VI) - Second step of data analysis</a> of the documentation), residing within the folder <code>properties</code>, accomplished by the <code>extract_properties</code> function in the script <code><a href="https://github.com/CEA-MetroCarac/PySSPFM/blob/main/PySSPFM/utils/nanoloop_to_hyst/file.py">utils/nanoloop_to_hyst/file.py</a></code>. The property selected by the user through the <code>'meas key'</code> parameter, serving as a sorting reference, is then singled out among all others. The extraction of measurement parameters from the csv measurement sheet is carried with <code>csv_meas_sheet_extract</code> function of the script <code><a href="https://github.com/CEA-MetroCarac/PySSPFM/blob/main/PySSPFM/utils/raw_extraction.py">utils/raw_extraction.py</a></code>. The measurement files are then sorted under two scenarios: <br>
 &#8226 If the <code>list_pixels</code> parameter is <code>None</code>: based on values of the user-chosen reference property. <br>
 &#8226 If the <code>list_pixels</code> parameter is <code>[]</code>: according to the file index. If the list is empty, all pixels are considered; otherwise, only the indices listed are considered.
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