DiadFit 0.0.85__py3-none-any.whl → 0.0.90__py3-none-any.whl

DiadFit/importing_data_files.py

@@ -14,6 +14,70 @@ import datetime
 import calendar
 
 encode="ISO-8859-1"
+## GEt video mag
+
+# Function to check if "Video Image" is in the first line, considering variations
+def line_contains_video_image(line):
+    """ This function returns video image information """
+    return "video image" in line.lower()
+    
+
+def get_video_mag(metadata_path):
+    """ This function finds all the video files in a single folder, and returns a dataframe of the filename and the magnification used. 
+    """
+    folder_path=metadata_path
+    data=[]
+    
+    
+    # Code below this
+    
+    
+    
+    # Ensure the directory exists and contains files
+    if os.path.exists(folder_path) and os.path.isdir(folder_path):
+        # Go through each file in the folder
+        for filename in os.listdir(folder_path):
+            if filename.endswith('.txt'):  # Confirming it's a text file
+                file_path = os.path.join(folder_path, filename)
+                with open(file_path, 'r', encoding="ISO-8859-1") as file:
+                    first_line = file.readline()
+                    # Initialize placeholders for magnification, width, and height
+                    magnification = None
+                    image_width = None
+                    image_height = None
+                    
+                    if "video image" in first_line.lower():  # Checks if "Video Image" is in the line
+                        for line in file:
+                            if "Objective Magnification:" in line:
+                                magnification = line.split(":")[-1].strip()
+                            elif "Image Width [µm]:" in line:
+                                image_width = line.split(":")[-1].strip()
+                            elif "Image Height [µm]:" in line:
+                                image_height = line.split(":")[-1].strip()
+                                
+                        # Add to data if magnification is found (assuming it's mandatory)
+                        if magnification:
+                            data.append({
+                                "Filename": filename,
+                                "Mag": magnification,
+                                "Width (µm)": image_width,
+                                "Height (µm)": image_height
+                            })
+    else:
+        print(f"The specified path {folder_path} does not exist or is not a directory.")
+    
+    # Create a DataFrame from the data
+    df = pd.DataFrame(data)
+    
+    # Display the DataFrame or a message if empty
+    if not df.empty:
+        return df
+    else:
+        print("No data found. Please check the folder path and the content of the files.")
+
+
+
+
 
 ## Functions for getting file names
 
@@ -37,7 +101,7 @@ def check_for_duplicates(spectra_path, prefix=True, prefix_str=' ', exception=Tr
 
     All_files_spectra= [f for f in listdir(spectra_path) if isfile(join(spectra_path, f))]
 
-    file_m=np.empty(len(All_files_spectra), dtype=object)
+    file_m=np.zeros(len(All_files_spectra), dtype=object)
     for i in range(0, len(All_files_spectra)):
         name=All_files_spectra[i]
         # If no prefix or suffix to remove, simple
@@ -129,6 +193,8 @@ def get_all_txt_files(path):
         if '.txt' in file and 'pandas' not in file:
             All_files.append(format(file))
     return All_files
+    
+# Function to get magnification of 
 
 
 ## Functions to just simply get data to plot up
@@ -925,14 +991,14 @@ def stitch_metadata_in_loop_witec(*, Allfiles, path, prefix=True, trupower=False
     date_str=[]
     month_str=[]
     # Numerical values
-    Int_time=np.empty(len(Allfiles), dtype=float)
-    objec=np.empty(len(Allfiles), dtype=float)
-    time=np.empty(len(Allfiles), dtype=float)
+    Int_time=np.zeros(len(Allfiles), dtype=float)
+    objec=np.zeros(len(Allfiles), dtype=float)
+    time=np.zeros(len(Allfiles), dtype=float)
 
-    Day=np.empty(len(Allfiles), dtype=float)
-    power=np.empty(len(Allfiles), dtype=float)
-    accumulations=np.empty(len(Allfiles), dtype=float)
-    spectral_cent=np.empty(len(Allfiles), dtype=float)
+    Day=np.zeros(len(Allfiles), dtype=float)
+    power=np.zeros(len(Allfiles), dtype=float)
+    accumulations=np.zeros(len(Allfiles), dtype=float)
+    spectral_cent=np.zeros(len(Allfiles), dtype=float)
 
     for i in tqdm(range(0, len(Allfiles))):
         filename1=Allfiles[i] #.rsplit('.',1)[0]
@@ -1081,7 +1147,7 @@ def extracting_filenames_generic(*, names, prefix=False,
 
     file_m=list(names)
 
-    file_m=np.empty(len(names), dtype=object)
+    file_m=np.zeros(len(names), dtype=object)
     for i in range(0, len(names)):
         name=names.iloc[i]
         # If no prefix or suffix to remove, simple
@@ -1126,12 +1192,12 @@ def extract_temp_Aranet(df):
     """ Extracts temperature data from the aranet
     """
     TD=str(Temp['Time(dd/mm/yyyy)'])
-    hour=np.empty(len(Temp), dtype=object)
-    date=np.empty(len(Temp), dtype=object)
-    time=np.empty(len(Temp), dtype=object)
-    minutes=np.empty(len(Temp), dtype=object)
-    seconds=np.empty(len(Temp), dtype=object)
-    secs_sm=np.empty(len(Temp), dtype=object)
+    hour=np.zeros(len(Temp), dtype=object)
+    date=np.zeros(len(Temp), dtype=object)
+    time=np.zeros(len(Temp), dtype=object)
+    minutes=np.zeros(len(Temp), dtype=object)
+    seconds=np.zeros(len(Temp), dtype=object)
+    secs_sm=np.zeros(len(Temp), dtype=object)
     for i in range(0, len(Temp)):
         TD=str(Temp['Time(dd/mm/yyyy)'].iloc[i])
         date[i]=TD.split(' ')[0]

DiadFit/ne_lines.py

@@ -46,7 +46,16 @@ error_pk2
     dist = (df['Raman_shift (cm-1)'] - line1_shift).abs()
     return df.loc[dist.idxmin()]
 
-
+def find_max_row(df, target_shift, tol=2):
+    """ This function is used to find the highest amplitude within a predefined ampl range for finding the right Ne line
+    """
+    
+    df_filtered = df[(df['Raman_shift (cm-1)'] >= target_shift - tol) & (df['Raman_shift (cm-1)'] <= target_shift + tol)]
+    
+    # Find the row with the maximum intensity within this filtered DataFrame
+    max_intensity_row = df_filtered.loc[df_filtered['Intensity'].idxmax()]
+    
+    return max_intensity_row
 
 def calculate_Ne_splitting(wavelength=532.05, line1_shift=1117, line2_shift=1447, cut_off_intensity=2000):
     """
@@ -72,23 +81,48 @@ def calculate_Ne_splitting(wavelength=532.05, line1_shift=1117, line2_shift=1447
     """
 
     df_Ne=calculate_Ne_line_positions(wavelength=wavelength, cut_off_intensity=cut_off_intensity)
-
-    closest1=find_closest(df_Ne, line1_shift).loc['Raman_shift (cm-1)']
-    closest2=find_closest(df_Ne, line2_shift).loc['Raman_shift (cm-1)']
-    closest_1_int=find_closest(df_Ne, line1_shift).loc['Intensity']
-    closest_2_int=find_closest(df_Ne, line2_shift).loc['Intensity']
-
-    diff=abs(closest1-closest2)
-
-    df=pd.DataFrame(data={'Ne_Split': diff,
+    # 
+    # closest1=find_closest(df_Ne, line1_shift).loc['Raman_shift (cm-1)']
+    # closest2=find_closest(df_Ne, line2_shift).loc['Raman_shift (cm-1)']
+    # closest_1_int=find_closest(df_Ne, line1_shift).loc['Intensity']
+    # closest_2_int=find_closest(df_Ne, line2_shift).loc['Intensity']
+    # 
+    # diff=abs(closest1-closest2)
+    # 
+    # df=pd.DataFrame(data={'Ne_Split': diff,
+    # 'Line_1': closest1,
+    # 'Line_2': closest2,
+    # 'Line_1_int': closest_1_int,
+    # 'Line_2_int': closest_2_int,
+    # 'Entered Pos Line 1': line1_shift,
+    # 'Entered Pos Line 2': line2_shift}, index=[0])
+    # 
+    # 
+    # return df
+# Use the new function to find the lines of interest
+    closest1_row = find_max_row(df_Ne, line1_shift)
+    closest2_row = find_max_row(df_Ne, line2_shift)
+    
+    # Extract the required values from the rows
+    closest1 = closest1_row['Raman_shift (cm-1)']
+    closest2 = closest2_row['Raman_shift (cm-1)']
+    closest_1_int = closest1_row['Intensity']
+    closest_2_int = closest2_row['Intensity']
+    
+    # Calculate the difference
+    diff = abs(closest1 - closest2)
+    
+    # Create the DataFrame
+    df = pd.DataFrame(data={
+    'Ne_Split': diff,
     'Line_1': closest1,
     'Line_2': closest2,
     'Line_1_int': closest_1_int,
     'Line_2_int': closest_2_int,
     'Entered Pos Line 1': line1_shift,
-    'Entered Pos Line 2': line2_shift}, index=[0])
-
-
+    'Entered Pos Line 2': line2_shift
+    }, index=[0])
+    
     return df
 
 def calculate_Ne_line_positions(wavelength=532.05, cut_off_intensity=2000):
@@ -131,10 +165,7 @@ def calculate_Ne_line_positions(wavelength=532.05, cut_off_intensity=2000):
     553.36788,
     553.86510,
     555.90978,
-    556.24416,
-    
-    556.27662,
-    556.30531,
+
     
     
     
@@ -333,10 +364,7 @@ def calculate_Ne_line_positions(wavelength=532.05, cut_off_intensity=2000):
     750,
     500,
     350,
-    1500,
-    
-    5000,
-    750,
+
     
     
     
@@ -1728,8 +1756,8 @@ def filter_Ne_Line_neighbours(*, df_combo=None, Corr_factor=None, number_av=6, o
     """
     if df_combo is not None:
         Corr_factor=df_combo['Ne_Corr']
-    Corr_factor_Filt=np.empty(len(Corr_factor), dtype=float)
-    median_loop=np.empty(len(Corr_factor), dtype=float)
+    Corr_factor_Filt=np.zeros(len(Corr_factor), dtype=float)
+    median_loop=np.zeros(len(Corr_factor), dtype=float)
 
     for i in range(0, len(Corr_factor)):
         if i<len(Corr_factor)/2: # For first half, do 5 after

{DiadFit-0.0.85.dist-info → DiadFit-0.0.90.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: DiadFit
-Version: 0.0.85
+Version: 0.0.90
 Summary: DiadFit
 Home-page: https://github.com/PennyWieser/DiadFit
 Author: Penny Wieser

DiadFit-0.0.90.dist-info/RECORD

@@ -0,0 +1,50 @@
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DiadFit-0.0.85.dist-info/RECORD

@@ -1,42 +0,0 @@
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-DiadFit/_version.py,sha256=hIfQHxP44V4g0sYEP6Hi4ni7quBcHy8sikP5VMQMXYk,296
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