Merge remote-tracking branch 'origin/dev_io_root' into dev_database

# Conflicts: # granddb/notestssh.py
grand-mother · Jun 6, 2024 · 883a5a6 · 883a5a6
2 parents 53d509e + 7c77b69
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diff --git a/.gitignore b/.gitignore
@@ -67,5 +67,5 @@ docs/apidoc-only/sphinx/source/grand.*
 # mac 
 .DS_Store
 
-*.pyc
-sim2root/CoREASRawRoot/__pycache__/CorsikaInfoFuncs.cpython-310.pyc
+
+
diff --git a/README.rst b/README.rst
@@ -14,8 +14,8 @@ Don't forget to initialize grand library before use it with script **env/setup.s
 
 .. code:: bash
    
-   $ pwd
-   .../grand
+   $ git clone https://github.com/grand-mother/grand.git
+   $ cd grand
    $ source env/setup.sh
 
 

diff --git a/env/_setup_env.sh b/env/_setup_env.sh
@@ -9,9 +9,15 @@ echo "add grand/quality to PATH"
 echo "=============================="
 
 export PATH=$GRAND_ROOT/scripts:$PATH
-echo "add grand/scripts to PATH "
+export PATH=$GRAND_ROOT/examples/dataio:$PATH
+echo "add scripts to PATH "
 echo "=============================="
 
 export PYTHONPATH=$GRAND_ROOT:$PYTHONPATH
 echo "add grand to PYTHONPATH"
 echo "=============================="
+
+
+export AIRESBINDIR=${HOME}/aires/bin
+echo "add AIRESBINDIR"
+echo "============================="
diff --git a/env/conda/grandlib_amd64.yml b/env/conda/grandlib_amd64.yml
@@ -1,4 +1,4 @@
-name: test_gr1
+name: /sps/grand/software/conda/grandlib_2304
 channels:
   - conda-forge
   - defaults
@@ -26,12 +26,13 @@ dependencies:
   - bzip2=1.0.8=h7f98852_4
   - c-ares=1.18.1=h7f98852_0
   - c-compiler=1.5.1=h166bdaf_0
-  - ca-certificates=2022.12.7=ha878542_0
+  - ca-certificates=2023.08.22=h06a4308_0
   - cairo=1.16.0=ha61ee94_1014
-  - certifi=2022.12.7=pyhd8ed1ab_0
+  - certifi=2023.7.22=py39h06a4308_0
   - cffi=1.15.1=py39he91dace_3
   - cfitsio=4.1.0=hd9d235c_0
   - charset-normalizer=2.1.1=pyhd8ed1ab_0
+  - cmake=3.22.1=h1fce559_0
   - colorama=0.4.6=pyhd8ed1ab_0
   - comm=0.1.2=pyhd8ed1ab_0
   - compilers=1.5.1=ha770c72_0
@@ -138,6 +139,7 @@ dependencies:
   - libtiff=4.4.0=h82bc61c_5
   - libtool=2.4.7=h27087fc_0
   - libuuid=2.32.1=h7f98852_1000
+  - libuv=1.44.2=h5eee18b_0
   - libwebp=1.2.4=h522a892_0
   - libwebp-base=1.2.4=h166bdaf_0
   - libxcb=1.13=h7f98852_1004
@@ -162,7 +164,7 @@ dependencies:
   - notebook-shim=0.2.2=pyhd8ed1ab_0
   - numba=0.56.4=py39h61ddf18_0
   - numpy=1.23.5=py39h3d75532_0
-  - openssl=3.0.7=h0b41bf4_2
+  - openssl=3.0.11=h7f8727e_2
   - packaging=23.0=pyhd8ed1ab_0
   - pandoc=2.19.2=h32600fe_1
   - pandocfilters=1.5.0=pyhd8ed1ab_0
@@ -201,6 +203,7 @@ dependencies:
   - requests=2.28.2=pyhd8ed1ab_0
   - rfc3339-validator=0.1.4=pyhd8ed1ab_0
   - rfc3986-validator=0.1.1=pyh9f0ad1d_0
+  - rhash=1.4.3=hdbd6064_0
   - root=6.26.10=py39h4661b88_1
   - root_base=6.26.10=py39h7695a35_1
   - scipy=1.10.0=py39h7360e5f_2
@@ -256,6 +259,11 @@ dependencies:
   - zlib=1.2.13=h166bdaf_4
   - zstd=1.5.2=h3eb15da_6
   - pip:
+      - appjar==0.94.0
+      - asdf==2.15.0
+      - asdf-standard==1.0.3
+      - asdf-transform-schemas==0.3.0
+      - asdf-unit-schemas==0.1.0
       - asteval==0.9.28
       - astroid==2.14.1
       - astropy==5.2.1
@@ -271,9 +279,11 @@ dependencies:
       - exceptiongroup==1.1.0
       - fonttools==4.38.0
       - future==0.18.3
+      - greenlet==2.0.2
       - h5py==3.8.0
       - iniconfig==2.0.0
       - isort==5.12.0
+      - jmespath==1.0.1
       - kiwisolver==1.4.4
       - lazy-object-proxy==1.9.0
       - lmfit==1.1.0
@@ -286,18 +296,23 @@ dependencies:
       - pathspec==0.11.0
       - pillow==9.4.0
       - pluggy==1.0.0
+      - psycopg2==2.9.6
       - py==1.11.0
       - pyerfa==2.0.0.1
       - pylint==2.16.1
       - pynacl==1.5.0
       - pyparsing==3.0.9
       - pytest==7.2.1
       - scp==0.14.5
+      - semantic-version==2.10.0
+      - showerradio==1.0.0
+      - sqlalchemy==2.0.9
+      - sshtunnel==0.4.0
       - tokenize-rt==5.0.0
       - toml==0.10.2
       - tomli==2.0.1
       - tomlkit==0.11.6
       - uncertainties==3.1.7
       - uproot==5.0.2
       - wrapt==1.14.1
-prefix: /home/jcolley/miniconda3/envs/test_gr1
+prefix: /sps/grand/software/conda/grandlib_2304
diff --git a/env/conda/readme.md b/env/conda/readme.md
@@ -1,5 +1,9 @@
 # GRANDLIB env with conda
 
+## Frequent confusion
+
+The conda environment **does not contain GRANDLIB code**. The conda environment installs the necessary libraries, executables, initializes environment variables to correctly compile the C part of GRANLIB (gull and turtle), please [constraints to use grandlib](https://github.com/grand-mother/grand/wiki#constraints-to-use-grandlib) in GRANDLIB wiki.
+
 ## WARNING
 
  * A wifi connection is not recommended for this installation
@@ -13,7 +17,7 @@ You need to have conda command installed, the minimal package to have it is mini
 
 [CLI conda environnement](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html)
 
-conda cheatsheet PDF: file:///home/jcolley/T%C3%A9l%C3%A9chargements/conda-cheatsheet-1.pdf
+[Conda cheat sheet PDF](https://docs.conda.io/projects/conda/en/4.6.0/_downloads/52a95608c49671267e40c689e0bc00ca/conda-cheatsheet.pdf)
 
 ## Some conda commands
 
@@ -53,9 +57,11 @@ conda activate grandlib
 
 
 Initialize GRANDLIB package and GULL/TURTLE compilation, in 
-the root package, do 
+the root package, first clone the package grand
 
 ```
+git clone https://github.com/grand-mother/grand.git
+cd grand
 source env/setup.sh
 ```
 
@@ -67,4 +73,4 @@ grand_quality_test_cov.bash
 ```
 
 
-If you encounter a problem write a ticket [here](https://github.com/grand-mother/collaboration-issues/issues)
+If you encounter a problem write a ticket [here](https://github.com/grand-mother/collaboration-issues/issues)
diff --git a/env/docker_fedo/.gitignore b/env/docker_fedo/.gitignore
diff --git a/env/docker_root/.gitignore b/env/docker_root/.gitignore
diff --git a/env/readme.md b/env/readme.md
@@ -1,12 +1,19 @@
-# GRAND environnement configuration
+# GRAND environment configuration
 
 
-## With docker
+## With Docker
 
-See github [wiki](https://github.com/grand-mother/grand/wiki) of grand project
 
+Docker is the best choice for Mac OS. Note image version depends on [processor architecture](https://hub.docker.com/r/grandlib/dev):
 
+* ARM64: for M1, M2 version 2.0
+* AMD64 : version 1.2
 
-## With conda 
+See github [wiki](https://github.com/grand-mother/grand/wiki#development-environment) of grand project
+
+
+## With Conda 
+
+Conda envionment is the best choice for linux.
 
 See conda [readme](conda/readme.md)
diff --git a/examples/basis/class_Handling3dTraces.ipynb b/examples/basis/class_Handling3dTraces.ipynb
diff --git a/examples/dataio/ioroot_3dtraces.py b/examples/dataio/ioroot_3dtraces.py
@@ -1,8 +1,8 @@
 #! /usr/bin/env python3
 
 import argparse
-from grand.dataio.root_files import get_file_event, get_ttree_in_file
-from grand.basis.traces_event import Handling3dTracesOfEvent
+from grand.dataio.root_files import get_file_event, _get_ttree_in_file
+from grand.basis.traces_event import Handling3dTraces
 import grand.manage_log as mlg
 import matplotlib.pylab as plt
 
@@ -41,6 +41,12 @@ def manage_args():
         help="plot trace x,y,z and power spectrum of detector unit (DU)",
         default=-100,
     )
+    parser.add_argument(
+        "--idx_evt",
+        type=int,
+        help="Select event with index <idx_evt>, given by -i option, idx_evt is always > 0 or = 0",
+        default=-100,
+    )
     parser.add_argument(
         "--trace_image",
         action="store_true",
@@ -64,14 +70,14 @@ def manage_args():
         type=int,
         default=-100,
         help="dump trace of DU",
-    )    # retrieve argument
+    )  # retrieve argument
     parser.add_argument(
         "-i",
         "--info",
         action="store_true",
         required=False,
         help="some information about the contents of the file",
-    )    # retrieve argument
+    )  # retrieve argument
     return parser.parse_args()
 
 
@@ -81,39 +87,53 @@ def main():
 
     args = manage_args()
     d_event = get_file_event(args.file.name)
+    if args.idx_evt != -100:
+        if args.idx_evt < 0:
+            logger.error("index events must >= 0")
+            return
+        if args.idx_evt >= d_event.get_nb_events():
+            logger.error(f"index events must < {d_event.get_nb_events()}")
+            return
+        d_event.load_event_idx(args.idx_evt)
     o_tevent = d_event.get_obj_handling3dtraces()
     if args.info:
         print(f"Nb events     : {d_event.get_nb_events()}")
+        print("Idx\trun_nb\tevent_nb")
+        for idx, evt in enumerate(d_event.l_events):
+            print(f"{idx}\t{evt[1]}\t{evt[0]}")
+        print(f"Select event index: {d_event.idx_event}")
+        print("===================")
         print(f"Nb DU         : {d_event.get_du_count()}")
         print(f"Size trace    : {d_event.get_size_trace()}")
-        print(f"TTree         : {get_ttree_in_file(args.file.name)}")
-    assert isinstance(o_tevent, Handling3dTracesOfEvent)
+
+    assert isinstance(o_tevent, Handling3dTraces)
     if args.list_du:
-        print(f"Identifier DU : {o_tevent.d_idxdu.keys()}")
+        print(f"Identifier DU : {o_tevent.idx2idt}")
     if args.trace_image:
         o_tevent.plot_all_traces_as_image()
     if args.footprint:
+        o_tevent.plot_footprint_4d_max()
         o_tevent.plot_footprint_val_max()
     if args.time_val:
-        o_tevent.plot_footprint_val_max_inter()
+        o_tevent.plot_footprint_time_slider()
     if args.trace != -100:
-        if not args.trace in o_tevent.d_idxdu.keys():
+        if not args.trace in o_tevent.idt2idx.keys():
             logger.error(f"ERROR: unknown DU identifer")
             return
         o_tevent.plot_trace_du(args.trace)
-        o_tevent.plot_ps_trace_du(args.trace)
+        o_tevent.plot_psd_trace_du(args.trace)
     if args.list_ttree:
-        print(get_ttree_in_file(args.file.name))
+        print(_get_ttree_in_file(args.file.name))
     if args.dump != -100:
-        if not args.dump in o_tevent.d_idxdu.keys():
+        if not args.dump in o_tevent.idt2idx.keys():
             logger.error(f"ERROR: unknown DU identifer")
             return
-        idx_du = o_tevent.d_idxdu[args.dump]
+        idx_du = o_tevent.idt2idx[args.dump]
         tr_du = o_tevent.traces[idx_du]
         t_tr = o_tevent.t_samples[idx_du]
         for idx in range(o_tevent.get_size_trace()):
             print(f"{t_tr[idx]} {tr_du[0,idx]} {tr_du[1,idx]} {tr_du[2,idx]}")
-        
+
 
 if __name__ == "__main__":
     logger.info(mlg.string_begin_script())