Mercurial > public > atmospheric_lidar / changeset

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docs/Makefile	Thu Dec 07 16:54:41 2017 +0200
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = Atmosphericlidar
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docs/apidocs.rst	Thu Dec 07 16:54:41 2017 +0200
@@ -0,0 +1,28 @@
+API documentation
+=================
+
+
+Generic classes
+---------------
+.. automodule:: atmospheric_lidar.generic
+   :members:
+
+
+Licel-specific classes
+----------------------
+.. automodule:: atmospheric_lidar.licel
+   :members:
+
+
+Scripts
+-------
+
+licel2scc
+~~~~~~~~~
+.. automodule:: atmospheric_lidar.scripts.licel2scc
+   :members:
+
+licel2scc_depol
+~~~~~~~~~~~~~~~
+.. automodule:: atmospheric_lidar.scripts.licel2scc_depol
+   :members:

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docs/conf.py	Thu Dec 07 16:54:41 2017 +0200
@@ -0,0 +1,196 @@
+# -*- coding: utf-8 -*-
+#
+# Atmospheric lidar documentation build configuration file, created by
+# sphinx-quickstart on Thu Dec  7 15:45:39 2017.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../'))
+
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ['sphinx.ext.autodoc',
+            'sphinx.ext.intersphinx',
+            'sphinx.ext.todo',
+            'sphinx.ext.mathjax',
+            'sphinx.ext.viewcode']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'Atmospheric lidar'
+copyright = u'2017, Ioannis Binietoglou, Victor Nicolae'
+author = u'Ioannis Binietoglou, Victor Nicolae'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = u'0.2.11'
+# The full version, including alpha/beta/rc tags.
+release = u'0.2.11'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# This is required for the alabaster theme
+# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
+html_sidebars = {
+    '**': [
+        'relations.html',  # needs 'show_related': True theme option to display
+        'searchbox.html',
+    ]
+}
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'Atmosphericlidardoc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'Atmosphericlidar.tex', u'Atmospheric lidar Documentation',
+     u'Ioannis Binietoglou, Victor Nicolae', 'manual'),
+]
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'atmosphericlidar', u'Atmospheric lidar Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'Atmosphericlidar', u'Atmospheric lidar Documentation',
+     author, 'Atmosphericlidar', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+
+# -- Options for Epub output ----------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+epub_author = author
+epub_publisher = author
+epub_copyright = copyright
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']
+
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'https://docs.python.org/': None}

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docs/index.rst	Thu Dec 07 16:54:41 2017 +0200
@@ -0,0 +1,23 @@
+.. Atmospheric lidar documentation master file, created by
+   sphinx-quickstart on Thu Dec  7 15:45:39 2017.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to Atmospheric lidar's documentation!
+=============================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   introduction
+   apidocs
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docs/introduction.rst	Thu Dec 07 16:54:41 2017 +0200
@@ -0,0 +1,181 @@
+Overview
+========
+
+This package provides utilities to handle raw (atmospheric) lidar input data.
+The main format supported are Licel binary files (including the Raymetrics modified format).
+
+The package provides a single command line tool, called licel2scc that can convert Licel binary files to the
+EARLINET's Single Calculus Chain NetCDF format.
+
+Installation
+------------
+
+The easiest way to install this module is from the python package index using ``pip``::
+
+   pip install atmospheric-lidar
+
+Using it as a Licel to SCC converter
+------------------------------------
+
+Parameter file
+~~~~~~~~~~~~~~
+Before converting Licel binary to SCC format, you need to create a file linking Licel channels to SCC channels.
+
+As an example, you can start by changing the file “cf_netcdf_parameters.py” that describe such
+parameters for the Clermont Ferrand  lidar.
+
+Command line interface
+~~~~~~~~~~~~~~~~~~~~~~
+The usage of the  ``licel2scc`` program is described below::
+
+    A program to convert Licel binary files to the SCC NetCDF format.
+
+    positional arguments:
+      parameter_file        The path to a parameter file linking licel and SCC
+                            channels.
+      files                 Location of licel files. Use relative path and
+                            filename wildcards. (default './*.*')
+
+    optional arguments:
+      -h, --help            show this help message and exit
+      -i, --id_as_name      Use transient digitizer ids as channel names, instead
+                            of descriptive names
+      -m MEASUREMENT_ID, --measurement_id MEASUREMENT_ID
+                            The new measurement id
+      -n MEASUREMENT_NUMBER, --measurement_number MEASUREMENT_NUMBER
+                            The measurement number for the date from 00 to 99.
+                            Used if no id is provided
+      -t TEMPERATURE, --temperature TEMPERATURE
+                            The temperature (in C) at lidar level, required if
+                            using US Standard atmosphere
+      -p PRESSURE, --pressure PRESSURE
+                            The pressure (in hPa) at lidar level, required if
+                            using US Standard atmosphere
+      -D DARK_FILES, --dark_files DARK_FILES
+                            Location of files containing dark measurements.
+                            Use relative path and filename wildcars, see 'files'
+                            parameter for example.
+      -d, --debug           Print dubuging information.
+      -s, --silent          Show only warning and error messages.
+      --version             Show current version.
+
+Similarly, the ``licel2scc-depol`` program can be used to convert
+Licel files from Delta45 depolarization calibration measurements::
+
+    A program to convert Licel binary files from depolarization calibration
+    measurements to the SCC NetCDF format.
+
+    positional arguments:
+      parameter_file        The path to a parameter file linking licel and SCC
+                            channels.
+      plus45_string         Search string for plus 45 degree files (default '*.*')
+      minus45_string        Search string for minus 45 degree files (default
+                            '*.*')
+
+    optional arguments:
+      -h, --help            show this help message and exit
+      -i, --id_as_name      Use transient digitizer ids as channel names, instead
+                            of descriptive names
+      -m MEASUREMENT_ID, --measurement_id MEASUREMENT_ID
+                            The new measurement id
+      -n MEASUREMENT_NUMBER, --measurement_number MEASUREMENT_NUMBER
+                            The measurement number for the date from 00 to 99.
+                            Used if no id is provided
+      -t TEMPERATURE, --temperature TEMPERATURE
+                            The temperature (in C) at lidar level, required if
+                            using US Standard atmosphere
+      -p PRESSURE, --pressure PRESSURE
+                            The pressure (in hPa) at lidar level, required if
+                            using US Standard atmosphere
+      -d, --debug           Print dubuging information.
+      -s, --silent          Show only warning and error messages.
+      --version             Show current version.
+
+Usage in python code
+--------------------
+System class
+~~~~~~~~~~~~
+To read data from a system, you need create a class that describes you system.
+This is very simple if your lidar data are in the Licel format, as you only need to specify
+the external file with the extra SCC parameters. You can use as an example the file ``cf_netcdf_parameters.py``:
+
+.. code-block:: python
+
+   from licel import LicelLidarMeasurement
+   import cf_netcdf_parameters
+
+   class CfLidarMeasurement(LicelLidarMeasurement):
+       extra_netcdf_parameters = cf_netcdf_parameters
+
+This code assumes that the ``cf_netcdf_parameters.py`` is in your python path.
+
+Using the class
+~~~~~~~~~~~~~~~
+
+Once you have made the above setup you can start using it. The best way to understand how
+it works is through an interactive shell (I suggest [ipython](http://ipython.org/)).
+In the following example I use the cf_raymetrics setup:
+
+.. code-block:: python
+
+   import glob  # This is needed to read a list of filenames
+   import cf_lidar
+
+   # Go to the folder where you files are stored
+   cd /path/to/lidar/files
+
+   # Read the filenames
+   files  = glob.glob("*") # The * reads all the files in the folder.
+
+   # Read the files
+   my_measurement = cf_lidar.CfLidarMeasurement(files)
+
+   # Now the data have been read, and you have a measurement object to work with:
+   # See what channels are present
+   print(my_measurement.channels)
+
+   # Quicklooks of all the channels
+   my_measurements.plot()
+
+Converting to SCC format
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+There are some extra info you need to put in before converting to SCC format, "Measurement_ID", "Temperature", "Pressure":
+
+.. code-block:: python
+
+   my_measurement.info["Measurement_ID"] = "20101229op00"
+   my_measurement.info["Temperature"] = "14"
+   my_measurement.info["Pressure"] = "1010"
+
+You can use standard values of temperature and pressure by just calling:
+
+.. code-block:: python
+
+    my_measurement.get_PT()
+
+You can specify the standard values by overriding your system's ``get_PT`` method:
+
+.. code-block:: python
+
+   from licel import LicelLidarMeasurement
+   import cf_netcdf_parameters
+
+   class CfLidarMeasurement(LicelLidarMeasurement):
+       extra_netcdf_parameters = cf_netcdf_parameters
+
+       def get_PT():
+           self.info['Temperature'] = 25.0
+           self.info['Pressure'] = 1020.0
+
+If you have an external source of temperature and pressure information (a meteorological station) you can automate
+this by reading the appropriate code in the ``get_PT`` method .
+
+
+After you have used this extra input, you save the file using this command:
+
+.. code-block:: python
+
+   my_measurement.save_as_SCC_netcdf("filename")
+
+where you change the output filename to the filename you want to use.
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docs/make.bat	Thu Dec 07 16:54:41 2017 +0200
@@ -0,0 +1,36 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+set SPHINXPROJ=Atmosphericlidar
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd