ENH : Add a script to generate configuration file (with user's interractions)

python_src/ex_config/ex_config_diapOTB_Cosmo.json

@@ -45,7 +45,7 @@
 	    "GridStep_azimut": 150,
 	    "Grid_Threshold": 0.3,
 	    "Grid_Gap": 3000,
-	    "Interferogram_gain": 0.1,
+	    "Interferogram_gain": 0.1
 	}
     },
     "Post_Processing":

python_src/utils/func_utils.py

@@ -621,6 +621,14 @@ def str2bool(v):
     """
     return v.lower() in ("yes", "true", "t", "1") 
 
+
+def avoidDuplicates(inlist):
+    """
+        Remove duplicates into an input list.
+    """
+    outlist = list(dict.fromkeys(inlist))
+    return outlist
+
 def check_ifExist(fileOrPathOrImg):
     """
         Check if a file, path or image exists. If not quit the program.
@@ -630,6 +638,14 @@ def check_ifExist(fileOrPathOrImg):
         quit()
 
 
+def check_ifDir(inDir):
+    """
+        Check if the input path exists and is a directory
+    """
+    if not os.path.isdir(inDir):
+        print(inDir + " does not exists or is not a directory")
+        quit()
+
 def check_burstIndex(burst_index):
     """
         Check if the burst_index as string input is correctly sent

python_src/utils/generateConfigFile.py

+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+""" 
+    generateConfigFile.py
+    =====================
+
+    Python script to generate configuration file (json format) with default parameters and user's paths
+ 
+"""
+
+import os
+import re
+import json
+import readline, glob
+
+import func_utils
+
+# Util fct for autocompletion
+def complete(text, state):
+    return (glob.glob(text+'*')+[None])[state]
+
+
+# Questions to user for SAR_MultiSlc* chains
+def askForMultiSlc(dataConfig) :
+    # Select sensor if SAR_MultiSlc
+    sensor = "S1IW"
+    if (response == "SAR_MultiSlc") :
+        sensor = input("Please, select the wanted sensor S1SM " \
+                       "(for Sentinel-1 StripMap mode) or Cosmo " \
+                       "(for Cosmo-Skymed Spotligth and StriMap mode) : " )
+
+        if sensor not in ["S1SM", "Cosmo"] :
+            print("Unknown sensor, please choose between S1SM or Cosmo")
+            quit()
+
+    # SRTM_Shapefile
+    SRTM_Shapefile = os.path.realpath(input("Please, enter your path to srtm shp : " ))
+    func_utils.check_ifExist(SRTM_Shapefile)
+
+    # SRTM_Path
+    SRTM_Path = os.path.realpath(input("Please, enter your path to srtm hgt files : " ))
+    func_utils.check_ifDir(SRTM_Path)
+
+    # Input/Output Paths
+    Input_Path = os.path.realpath(input("Please, enter your path to input images : " ))
+    func_utils.check_ifDir(Input_Path)
+
+    Output_Path = os.path.realpath(input("Where would you like to store the output results : " ))
+    #func_utils.check_ifDir(os.path.dirname(Output_Path))
+    func_utils.check_ifDir(Output_Path)
+
+    # reference image (must be into Input_Path)
+    reference_image = input("Which image is your reference : " )
+    func_utils.check_ifExist(reference_image)
+    reference_image = os.path.basename(reference_image)
+
+    if not func_utils.get_imgFromDir(reference_image, Input_Path) :
+        print(reference_image + " not found into given input path " + \
+              "Input_Path")
+        print("Please check your input path")
+        quit()
+    else :
+        correct = func_utils.check_image_pattern(reference_image, mode=sensor)
+        if not correct : 
+            print("Reference image " + reference_image + " does not respect naming conventions for the " \
+                  "selected sensor")
+            quit()
+
+    # Geoid file
+    res_geoid = input("Would you like to add a geoid file (yes/no) : ")
+    Geoid = None
+
+    if res_geoid == "yes" :
+        Geoid = os.path.realpath(input("Please, enter your path to your geoid file : "))
+        func_utils.check_ifExist(Geoid)
+    else :
+        Geoid = os.getenv('OTB_GEOID_FILE')
+
+    # Start/End date for image selection
+    res_date = input("Would you like to specify a start and end date for image selection (yes/no) : ")
+
+    # Dummy dates to select by default all images into Input_Path
+    start_date = "19000101"
+    end_date = "29000101"
+    pattern = "".join(['\d{8}'])
+    if res_date == "yes" :
+        start_date = input("Please, indicate a start date with YYYYMMDD format : ")
+        if not re.match(pattern, start_date) :
+            print("start_date " + start_date + " does not respect the expected format YYYYMMDD")
+            quit()
+
+        end_date = input("Please, indicate a end date with YYYYMMDD format : ")
+        if not re.match(pattern, end_date) :
+            print("end_date " + end_date + " does not respect the expected format YYYYMMDD")
+            quit()
+
+    # Indicate to user, all selected images with given dates, polarisation and input_path
+    ext = "tiff"
+    pol = ""
+    iw = ""
+    if sensor == "Cosmo" :
+        ext = "h5"
+        pol = reference_image.split("_")[5]
+    else :
+        pol = reference_image.split("-")[3]
+
+    if sensor == "S1IW" :
+        iw = reference_image.split("-")[1]
+        ext = ""
+
+    exclude = "-9999"
+    tiff_list, throw_warning = func_utils.get_AllTiff(pol=pol, ext=ext, iw=iw, searchDir=Input_Path)
+    tiff_dates = func_utils.get_Tiff_WithDates(int(start_date), int(end_date), exclude, tiff_list, ext)
+
+    # Avoid duplicates 
+    tiff_dates = func_utils.avoidDuplicates(tiff_dates)
+    tiff_dates.remove(reference_image)
+
+    print("For your information, the selected images for processings will be : ")
+    print("As reference : " + reference_image)
+    print("As secondaries : " + str(tiff_dates))
+
+    # Ask to continue if selection OK
+    res_continue = input("Do you agree to continue with this selection (yes/no) : ")
+
+    if res_continue != "yes" :
+        print("Previous selection does not correspond to your expectations, you can relaunch this script with new inputs")
+        quit()
+
+    # EOF file
+    EOF_Path = None
+    if sensor != "Cosmo" :
+        res_eof = input("Would you like to indicate fine orbits (yes/no) : ")
+
+        if res_eof == "yes" : 
+            EOF_Path = os.path.realpath(input("Please, enter your path to .EOF files : " ))
+            func_utils.check_ifDir(EOF_Path)
+
+
+    # Fill with user's response our generic fields for SAR_MultiSlc* chains
+    dataConfig['Global']['in']['SRTM_Shapefile'] = SRTM_Shapefile
+    dataConfig['Global']['in']['SRTM_Path'] = SRTM_Path
+    dataConfig['Global']['in']['Input_Path'] = Input_Path
+    dataConfig['Global']['in']['Master_Image'] = reference_image
+    dataConfig['Global']['in']['Start_Date'] = start_date
+    dataConfig['Global']['in']['End_Date'] = end_date
+    if Geoid :
+        dataConfig['Global']['in']['Geoid'] = Geoid
+    else :
+        del dataConfig['Global']['in']['Geoid']
+    if EOF_Path :
+        dataConfig['Global']['in']['EOF_Path'] = EOF_Path
+
+    dataConfig['Global']['out']['Output_Path'] = Output_Path    
+
+
+# Questions to user for diapOTB* chains
+def askForDiapOTB(dataConfig) :
+    # Select sensor if diapOTB
+    sensor = "S1IW"
+    if (response == "diapOTB") :
+        sensor = input("Please, select the wanted sensor S1SM " \
+                       "(for Sentinel-1 StripMap mode) or Cosmo " \
+                       "(for Cosmo-Skymed Spotligth and StriMap mode) : " )
+
+        if sensor not in ["S1SM", "Cosmo"] :
+            print("Unknown sensor, please choose between S1SM or Cosmo")
+            quit()
+
+        
+    # reference image (path to image)
+    reference_image = os.path.realpath(input("Which image is your reference : " ))
+    func_utils.check_ifExist(reference_image)
+    reference_image_base = os.path.basename(reference_image)
+
+    correct = func_utils.check_image_pattern(reference_image_base, mode=sensor)
+    if not correct : 
+        print("Reference image " + reference_image_base + " does not respect naming conventions for the " \
+              "selected sensor")
+        quit()
+
+    # reference image (path to image)
+    secondary_image = os.path.realpath(input("Which image is secondary : " ))
+    func_utils.check_ifExist(secondary_image)
+    secondary_image_base = os.path.basename(secondary_image)
+
+    correct = func_utils.check_image_pattern(secondary_image_base, mode=sensor)
+    if not correct : 
+        print("Reference image " + secondary_image_base + " does not respect naming conventions for the " \
+              "selected sensor")
+        quit()
+
+
+    # DEM Path
+    DEM_Path = os.path.realpath(input("Please, enter your path to your DEM : "))
+    func_utils.check_ifExist(DEM_Path)
+
+    # Output Path
+    Output_Path = os.path.realpath(input("Where would you like to store the output results : " ))
+    func_utils.check_ifDir(os.path.dirname(Output_Path))
+
+    # EOF file
+    EOF_Path = None
+    if sensor != "Cosmo" :
+        res_eof = input("Would you like to indicate fine orbits (yes/no) : ")
+
+        if res_eof == "yes" : 
+            EOF_Path = os.path.realpath(input("Please, enter your path to .EOF files : " ))
+            func_utils.check_ifDir(EOF_Path)
+
+
+    # Fill with user's response our generic fields for SAR_MultiSlc* chains
+    dataConfig['Global']['in']['Master_Image_Path'] = reference_image
+    dataConfig['Global']['in']['Slave_Image_Path'] = secondary_image
+    dataConfig['Global']['in']['DEM_Path'] = DEM_Path
+    if EOF_Path :
+        dataConfig['Global']['in']['EOF_Path'] = EOF_Path
+
+    dataConfig['Global']['out']['output_dir'] = Output_Path   
+
+
+
+###################
+###### Main #######
+###################
+if __name__ == "__main__":
+    
+    ######### Introduction prints #########
+    print("Welcome to DiapOTB remote module !")
+    print("You can generate configuration files for the four available processing chains : diapOTB," \
+          "diapOTB_S1IW, SAR_MultiSlc and SAR_MultiSlc_IW")
+    
+
+    ######### Load the example for prepare the configuration file according to user's choice #########
+    # First choice for user : the selected chain
+    response = input("Please, choose your porcessing chain (diapOTB, diapOTB_S1IW, SAR_MultiSlc and " \
+                     "SAR_MultiSlc_IW) : ")
+    
+    if response not in ['diapOTB', 'diapOTB_S1IW', 'SAR_MultiSlc', 'SAR_MultiSlc_IW'] : 
+        print("Wrong chain, please choose between available chains")
+        
+        
+    
+    # Load examples according to the selected chain => Init a dictionnary with default parameters
+    current_path = os.path.dirname(os.path.realpath(__file__))
+    ex_config_path = os.path.join(current_path, "../ex_config")
+   
+    dataConfig = {}
+    if response == "diapOTB" :
+        
+        ex_confile = os.path.join(ex_config_path, "ex_config_diapOTB_Cosmo.json") 
+        dataConfig = func_utils.load_configfile(ex_confile, "S1_SM")
+    
+    elif response == "diapOTB_S1IW" :
+
+        ex_confile = os.path.join(ex_config_path, "ex_config_diapOTB_S1IW.json") 
+        dataConfig = func_utils.load_configfile(ex_confile, "S1_IW")
+    
+    elif response == "SAR_MultiSlc" :
+
+        ex_confile = os.path.join(ex_config_path, "ex_config_MultiSlc_CosmoS1SM.json")
+        dataConfig = func_utils.load_configfile(ex_confile, "multi_S1")
+    
+    elif response == "SAR_MultiSlc_IW" :
+
+        ex_confile = os.path.join(ex_config_path, "ex_config_MultiSlc_IW.json")
+        dataConfig = func_utils.load_configfile(ex_confile, "multi_SW")
+
+
+
+    ########## Prepare for questions : with autocompletion #########
+    readline.set_completer_delims(' \t\n;')
+    readline.parse_and_bind("tab: complete")
+    readline.set_completer(complete)
+    
+    ########## Ask to user for generic fields #########
+    # SAR_MultiSlc* chains
+    if (response == "SAR_MultiSlc" or response == "SAR_MultiSlc_IW") : 
+        askForMultiSlc(dataConfig)
+        
+    if (response == "diapOTB" or response == "diapOTB_S1IW") : 
+        askForDiapOTB(dataConfig)
+    
+
+    # Dump dataConfig with the new fields and the default parameters
+    res_json = os.path.realpath(input("Where do you want store your configuration file : "))
+    
+    # if directory
+    if os.path.isdir(res_json) :
+        res_json_name = input("Please, enter a name for your configuration " \
+                              "file (with .json extension) : ")
+        
+        if os.path.exists(os.path.join(res_json, res_json_name)) :
+            res_json_overwrite = input("Would you like to overwrite the file " + 
+                                       res_json_name + " (yes/no) : ")
+            
+            if res_json_overwrite == "yes" :
+                with open(os.path.join(res_json, res_json_name), 'w') as f:
+                    json.dump(dataConfig, f, indent=2, sort_keys=False)
+            else :
+                print("Generation Aborted")
+                quit()
+
+        else :
+            with open(os.path.join(res_json, res_json_name), 'w') as f:
+                json.dump(dataConfig, f, indent=2, sort_keys=False)
+                
+    # If file (or wrong path)
+    else :
+        if os.path.isdir(os.path.dirname(res_json)) :
+            
+            if os.path.exists(res_json) :
+                res_json_overwrite = input("Would you like to overwrite the file " + 
+                                           res_json + " (yes/no) : ")
+            
+                if res_json_overwrite == "yes":
+                    with open(res_json, 'w') as f:
+                        json.dump(dataConfig, f, indent=2, sort_keys=False)
+                else :
+                    print("Generation Aborted")
+                    quit()
+            else :
+                with open(res_json, 'w') as f:
+                    json.dump(dataConfig, f, indent=2, sort_keys=False)
+
+        else :
+            print("Wrong path for the configuration file, Generation Aborted")
+            
+
+    ######### Conclusion prints #########
+    print("The configuration file was generated !")
+    print("You can modify the parameters in it and launch the processing chain with this file as only argument")
+    print("You can find further information on https://gitlab.orfeo-toolbox.org/remote_modules/diapotb/-/wikis/")
+        
+