Merge pull request #9 from fotobiolab-unb/optim

Updating with new optimization feature

.gitignore

@@ -0,0 +1,170 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+logs/
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.env.local
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+.vscode/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+cache.csv
+log/
+calibrate/
+experiment.py
+nohup.out

pyduino/__init__.py

@@ -1,9 +1,18 @@
 import logging
+import os
+from dotenv import load_dotenv
+
+load_dotenv()
+load_dotenv(dotenv_path=".env.local")
+
+log_file_path = os.environ.get('PYDUINO_SLAVE_LOG','/var/log/pyduino/slave.log')
+os.makedirs(os.path.dirname(log_file_path), exist_ok=True)
+
 logging.basicConfig(
     level=logging.DEBUG,
     format='%(asctime)s %(levelname)s %(message)s',
     handlers=[
-        logging.FileHandler('/var/log/pyduino/slave.log'),
+        logging.FileHandler(log_file_path),
         logging.StreamHandler()
     ]
 )

pyduino/config.yaml

@@ -1,67 +1,25 @@
 hyperparameters:
   reset_density: true #Whether or not to use gotod
-  log_name: "ga_dcte2400_branco_15" #Log folder name (delete to use the default)
-  f_param: efficiency #Parameter to read as fitness from the reactors
+  log_name: "free_growth_test_2024_04_07" #Log folder name (delete to use the default)
   density_param: DensidadeAtual #Parameter name for density counts
-  mutation_probability: 0.01 #0.15
-  maximize: true
-  resolution: 4 #Number of bits used for each parameter
-  elitism: true #Whether or not to use elitism
-  do_crossover: false #Whether or not to perform crossover when the genetic algorithm is enabled
-  rng_seed: 2 #Random seed for genetic algorithm
+  maximize: false
+  rng_seed: 2 #Random seed parameter initialization
   ranges:
     # brilho:
     #   - 0
     #   - 100
     branco:
       - 1
-      #- 100
-      - 19
-    full:
+      - 100                                     
+    others:
       - 0
-      #- 100
-      - 17
-    "440":
-      - 0
-      #- 100
-      - 26
-    "470":
-      - 0
-      #- 100
-      - 24
-    "495":
-      - 0
-      #- 100
-      - 24
-    "530":
-      - 0
-      #- 100
-      - 24
-    "595":
-      - 0
-      #- 100
-      - 92
-    "634":
-      - 0
-      #- 100
-      - 58
-    "660":
-      - 0
-      #- 100
-      - 44
-    "684":
-      - 0
-      #- 100
-      - 35                                          
-    #others:
-    #  - 0
-    #  - 100
+      - 100
 slave:
   port: "5000" #Must be a string
   network: "192.168.1.1/24"
-  exclude: "192.168.1.112"
+  exclude: #"192.168.1.112"
 system:
-  initial_state: "preset_state.d/no4.csv"
+  initial_state: "preset_state.d/all.csv"
   reboot_wait_time: 5 #Time in seconds to wait after a reboot.
   relevant_parameters:
     # - brilho
@@ -116,7 +74,7 @@ system:
     co2: int
     dtco2: int
 dash:
-  glob: "./log/pre_free1212_branco_3/*.csv"
+  glob: "./log/nelder_mead_power_test/*.csv"
   plot:
     - 
       name: Temperature
@@ -132,18 +90,18 @@ dash:
       name: Density
       cols:
         DensidadeAtual:
-    -
-      name: Efficiency
-      cols:
-        efficiency:
-          growing_only: true
-          #mode: 'lines+markers'
-    -
-      name: GrowthRate
-      cols:
-        growth_rate:
-          growing_only: true
-          #mode: 'lines+markers'
+    # -
+    #   name: Efficiency
+    #   cols:
+    #     efficiency:
+    #       growing_only: true
+    #       #mode: 'lines+markers'
+    # -
+    #   name: GrowthRate
+    #   cols:
+    #     growth_rate:
+    #       growing_only: true
+    #       #mode: 'lines+markers'
     -
       name: power
       cols:

pyduino/dashboard.py

@@ -40,7 +40,7 @@
 NROWSDF = y["tail"]
 if len(LOG_PATH)!=0:
     with open(LOG_PATH[0]) as file:
-        HEAD = pd.read_csv(io.StringIO(''.join([file.readline() for _ in range(2)])),sep=SEP)
+        HEAD = pd.read_csv(io.StringIO(''.join([file.readline() for _ in range(1)])),sep=SEP)
         print(HEAD)
         HEAD = HEAD.columns
 else: