Merge branch 'dev' into dev_io_root

# Conflicts:
#	grand/sim/efield2voltage.py
#	scripts/convert_efield2voltage.py
#	sim2root/Common/IllustrateSimPipe.py

README.rst

@@ -1,14 +1,20 @@
-grand package |workflow| |codecov| |docs| |appimage|
-====================================================
+GRANDlib
+========
+|workflow| |codecov| |docs| |appimage|
 
-*Core* `Python 3`_  *package for the offline software of the* `GRAND`_
+
+*Core* `Python 3`_  *package for the offline data handling and analysis for the* `GRAND`_
 *Collaboration.*
 
+.. contents:: Contents
+   :local:
+   :depth: 2
+
 
 Environment
 -----------
 
-GRAND library can be used under docker to define a correct environment, read `GRAND_wiki`_ for more information, else you must install `ROOT`_ library and compile `TURTLE`_ and `GULL`_ library under your computer.
+The GRAND library - **GRANDlib** - can be used under docker to define a correct environment, read `GRAND_wiki`_ for more information, else you must install `ROOT`_ library and compile `TURTLE`_ and `GULL`_ library under your computer.
 
 Don't forget to initialize grand library before use it with script **env/setup.sh** only in the root of the package
 
@@ -20,9 +26,14 @@ Don't forget to initialize grand library before use it with script **env/setup.s
 
 
 Documentation
------------ 
+-------------
+
+Check the `online documentation`_ for further details, but best study the examples.
 
-Check the `online documentation`_ for further details.
+Examples
+--------
+
+Examples and scripts can be found under *examples/* and *scripts/* subdirectories
 
 
 How to contribute
@@ -90,3 +101,25 @@ The GRAND software is distributed under the LGPL-3.0 license. See the provided
 
 .. |workflow| image:: https://github.com/grand-mother/grand/workflows/Tests/badge.svg
    :target: https://github.com/grand-mother/grand/actions?query=workflow%3ATests
+
+Citing
+------
+
+If you use GRANDlib in your work, we ask you that you please cite the following paper: R. Alves Batista et al., GRANDlib: A simulation pipeline for the Giant Radio Array for Neutrino Detection
+(GRAND) (arXiv:2408.10926).
+
+If you are citing GRANDlib in a document that will be uploaded to the arXiv, please consider using the LaTeX or BibTeX entries provided by INSPIRE (link here):
+
+.. code:: latex
+
+   @article{GRAND:2024atu,
+    author = "Alves Batista, Rafael and others",
+    collaboration = "GRAND",
+    title = "{GRANDlib: A simulation pipeline for the Giant Radio Array for Neutrino Detection (GRAND)}",
+    eprint = "2408.10926",
+    archivePrefix = "arXiv",
+    primaryClass = "astro-ph.IM",
+    month = "8",
+    year = "2024"
+   }
+

data/download_LFmap_grand.py

@@ -0,0 +1,72 @@
+#! /usr/bin/env python3
+
+'''
+Created on 19 juil. 2022
+
+@author: Jean-Marc Colley, CNRS/IN2P3/LPNHE
+
+'''
+import tarfile
+import os
+import sys
+import os.path as osp
+from urllib import request
+#TODO: add progressbar to grand lib
+#import progressbar
+
+from grand import GRAND_DATA_PATH, grand_add_path_data
+
+#LINK_MODEL = "https://forge.in2p3.fr/attachments/download/133380/grand_model_2207.tar.gz"
+#FILE_MODEL = "grand_model_2207.tar.gz"
+#LINK_MODEL = "https://forge.in2p3.fr/attachments/download/201909/grand_model_2306.tar.gz"
+#LINK_MODEL = "https://forge.in2p3.fr/attachments/download/251637/grand_model_190224.tar.gz"
+LINK_MODEL = "https://forge.in2p3.fr/attachments/download/326497/LFmap.tar.gz"
+FILE_MODEL = LINK_MODEL.split("/")[-1]
+# class MyProgressBar():
+#     def __init__(self):
+#         self.pbar = None
+#
+#     def __call__(self, block_num, block_size, total_size):
+#         if not self.pbar:
+#             self.pbar=progressbar.ProgressBar(maxval=total_size)
+#             self.pbar.start()
+#
+#         downloaded = block_num * block_size
+#         if downloaded < total_size:
+#             self.pbar.update(downloaded)
+#         else:
+#             self.pbar.finish()
+
+
+# 1- test if download is necessary
+if os.path.exists(grand_add_path_data('noise/LFmap')):
+    print("==============================")
+    print('Skip download LFmap files for Galactic noise simulations')
+    sys.exit(0)
+
+GRAND_DATA_PATH_1 = osp.join(grand_add_path_data('noise'))
+tar_file = osp.join(GRAND_DATA_PATH_1, FILE_MODEL)
+
+# 2- download
+print("==============================")
+print("Download LFmap model (~ 6.4 MB) for GRAND, please wait ...")
+try:
+    request.urlretrieve(LINK_MODEL, tar_file)
+    print("Successfully downloaded")
+except:
+    print(f"download failed {LINK_MODEL}")
+    sys.exit(1)
+
+# 3- extract
+print("==============================")
+print('Extract tar file')
+try:
+    my_tar = tarfile.open(tar_file)
+    my_tar.extractall(grand_add_path_data('noise'))
+    my_tar.close()
+    os.remove(tar_file)  # delete zipped file are extraction.
+except:
+    print(f"Extract failed '{tar_file}'")
+    sys.exit(1)
+print("LFmap model available in grand/data/noise directory !")
+sys.exit(0) 

data/download_data_grand.py

@@ -19,27 +19,11 @@
 #LINK_MODEL = "https://forge.in2p3.fr/attachments/download/133380/grand_model_2207.tar.gz"
 #FILE_MODEL = "grand_model_2207.tar.gz"
 #LINK_MODEL = "https://forge.in2p3.fr/attachments/download/201909/grand_model_2306.tar.gz"
-LINK_MODEL = "https://forge.in2p3.fr/attachments/download/211902/grand_model_2306.tar.gz"
+#LINK_MODEL = "https://forge.in2p3.fr/attachments/download/251637/grand_model_190224.tar.gz"
+LINK_MODEL = "https://forge.in2p3.fr/attachments/download/340302/grand_model_141124.tar.gz"
 FILE_MODEL = LINK_MODEL.split("/")[-1]
 
 
-# class MyProgressBar():
-#     def __init__(self):
-#         self.pbar = None
-#
-#     def __call__(self, block_num, block_size, total_size):
-#         if not self.pbar:
-#             self.pbar=progressbar.ProgressBar(maxval=total_size)
-#             self.pbar.start()
-#
-#         downloaded = block_num * block_size
-#         if downloaded < total_size:
-#             self.pbar.update(downloaded)
-#         else:
-#             self.pbar.finish()
-
-
-# 1- test if download is necessary
 if os.path.exists(grand_add_path_data('detector')):
     print("==============================")
     print('Skip download data model')
@@ -49,7 +33,7 @@
 
 # 2- download
 print("==============================")
-print("Download data model (~ 452MB) for GRAND, please wait ...")
+print("Download data model (~ 1GB) for GRAND, please wait ...")
 try:
     request.urlretrieve(LINK_MODEL, tar_file)
     print("Successfully downloaded")
@@ -69,4 +53,4 @@
     print(f"Extract failed '{tar_file}'")
     sys.exit(1)
 print("data model available in grand/data directory !")
-sys.exit(0) 
+sys.exit(0) 

data/download_grand_antenna_models.py

@@ -0,0 +1,60 @@
+#! /usr/bin/env python3
+
+'''
+Created on 19 juil. 2022
+
+@author: Jean-Marc Colley, CNRS/IN2P3/LPNHE
+
+'''
+import tarfile
+import os
+import sys
+import os.path as osp
+from urllib import request
+#TODO: add progressbar to grand lib
+#import progressbar
+
+from grand import GRAND_DATA_PATH, grand_add_path_data
+
+#LINK_MODEL = "https://forge.in2p3.fr/attachments/download/133380/grand_model_2207.tar.gz"
+#FILE_MODEL = "grand_model_2207.tar.gz"
+#LINK_MODEL = "https://forge.in2p3.fr/attachments/download/201909/grand_model_2306.tar.gz"
+#LINK_MODEL = "https://forge.in2p3.fr/attachments/download/251637/grand_model_190224.tar.gz"
+LINK_MODEL = "https://forge.in2p3.fr/attachments/download/340302/grand_model_141124.tar.gz"
+FILE_MODEL = LINK_MODEL.split("/")[-1]
+
+
+directory = grand_add_path_data('detector')
+specific_file = os.path.join(directory, 'Light_GP300Antenna_nec_Yarm_leff.npz') 
+
+# Check if the specific file exists in the directory
+if os.path.isfile(specific_file):
+    print("==============================")
+    print('Skip download Grand antenna models')
+    sys.exit(0)
+
+tar_file = osp.join(GRAND_DATA_PATH, FILE_MODEL)
+
+# 2- download
+print("==============================")
+print("Download antenna models, RFchain, Galactic noise (~ 1GB) for GRAND, please wait ...")
+try:
+    request.urlretrieve(LINK_MODEL, tar_file)
+    print("Successfully downloaded")
+except:
+    print(f"download failed {LINK_MODEL}")
+    sys.exit(1)
+
+# 3- extract
+print("==============================")
+print('Extract tar file')
+try:
+    my_tar = tarfile.open(tar_file)
+    my_tar.extractall(grand_add_path_data(''))
+    my_tar.close()
+    os.remove(tar_file)  # delete zipped file are extraction.
+except:
+    print(f"Extract failed '{tar_file}'")
+    sys.exit(1)
+print("Antenna models available in grand/data/detector directory !")
+sys.exit(0) 

data/download_new_RFchain_grand.py

@@ -0,0 +1,72 @@
+#! /usr/bin/env python3
+
+'''
+Created on 19 juil. 2022
+
+@author: Jean-Marc Colley, CNRS/IN2P3/LPNHE
+
+'''
+import tarfile
+import os
+import sys
+import os.path as osp
+from urllib import request
+#TODO: add progressbar to grand lib
+#import progressbar
+
+from grand import GRAND_DATA_PATH, grand_add_path_data
+
+#LINK_MODEL = "https://forge.in2p3.fr/attachments/download/133380/grand_model_2207.tar.gz"
+#FILE_MODEL = "grand_model_2207.tar.gz"
+#LINK_MODEL = "https://forge.in2p3.fr/attachments/download/201909/grand_model_2306.tar.gz"
+#LINK_MODEL = "https://forge.in2p3.fr/attachments/download/251637/grand_model_190224.tar.gz"
+LINK_MODEL = "https://forge.in2p3.fr/attachments/download/312643/RFchain_V3.tar.gz"
+FILE_MODEL = LINK_MODEL.split("/")[-1]
+# class MyProgressBar():
+#     def __init__(self):
+#         self.pbar = None
+#
+#     def __call__(self, block_num, block_size, total_size):
+#         if not self.pbar:
+#             self.pbar=progressbar.ProgressBar(maxval=total_size)
+#             self.pbar.start()
+#
+#         downloaded = block_num * block_size
+#         if downloaded < total_size:
+#             self.pbar.update(downloaded)
+#         else:
+#             self.pbar.finish()
+
+
+# 1- test if download is necessary
+if os.path.exists(grand_add_path_data('detector/RFchain_v2')):
+    print("==============================")
+    print('Skip download data model')
+    sys.exit(0)
+
+GRAND_DATA_PATH_1 = osp.join(grand_add_path_data('detector'))
+tar_file = osp.join(GRAND_DATA_PATH_1, FILE_MODEL)
+
+# 2- download
+print("==============================")
+print("Download new RFchain model (~ 450 KB) for GRAND, please wait ...")
+try:
+    request.urlretrieve(LINK_MODEL, tar_file)
+    print("Successfully downloaded")
+except:
+    print(f"download failed {LINK_MODEL}")
+    sys.exit(1)
+
+# 3- extract
+print("==============================")
+print('Extract tar file')
+try:
+    my_tar = tarfile.open(tar_file)
+    my_tar.extractall(grand_add_path_data('detector'))
+    my_tar.close()
+    os.remove(tar_file)  # delete zipped file are extraction.
+except:
+    print(f"Extract failed '{tar_file}'")
+    sys.exit(1)
+print("data model available in grand/data/detector directory !")
+sys.exit(0)