dtscalibration · bdestombe · Aug 8, 2023 · Jul 31, 2023 · Jul 31, 2023 · Jul 31, 2023
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -12,12 +12,16 @@ Added
 Fixed
 
 * Single-ended measurements with `fix_alpha` failed due to a bug introduced in v2.0.0 ([#173](https://github.com/dtscalibration/python-dts-calibration/pull/173)).
+* Fixes headers in example notebooks and their appearance in the docs
 
 Changed
 
 * Standardized parameter names. Reduced the freedom in choosing parameter names and dimension names in favor of simplifying the code.
 * Requiring netcdf4 >= 1.6.4
 * Optional dependencies of xarray that improve performance are now required by default.
+* variance_stokes_linear() does not default through zero anymore.
+* Refactored calibration_single_ended and calibration_double_ended()
+* Moved ParameterIndices classes to calibration_utils.py
 * Flox included in requirements to speed up resampling via xarray ([Xarray #5734](https://github.com/pydata/xarray/pull/5734)).
 
 Removed

diff --git a/docs/api/dtscalibration.DataStore.rst b/docs/api/dtscalibration.DataStore.rst
diff --git a/docs/api/dtscalibration.check_dims.rst b/docs/api/dtscalibration.check_dims.rst
diff --git a/docs/api/dtscalibration.check_timestep_allclose.rst b/docs/api/dtscalibration.check_timestep_allclose.rst
diff --git a/docs/api/dtscalibration.get_netcdf_encoding.rst b/docs/api/dtscalibration.get_netcdf_encoding.rst
diff --git a/docs/api/dtscalibration.merge_double_ended.rst b/docs/api/dtscalibration.merge_double_ended.rst
diff --git a/docs/api/dtscalibration.open_datastore.rst b/docs/api/dtscalibration.open_datastore.rst
diff --git a/docs/api/dtscalibration.open_mf_datastore.rst b/docs/api/dtscalibration.open_mf_datastore.rst
diff --git a/docs/api/dtscalibration.plot_accuracy.rst b/docs/api/dtscalibration.plot_accuracy.rst
diff --git a/docs/api/dtscalibration.plot_location_residuals_double_ended.rst b/docs/api/dtscalibration.plot_location_residuals_double_ended.rst
diff --git a/docs/api/dtscalibration.plot_residuals_reference_sections.rst b/docs/api/dtscalibration.plot_residuals_reference_sections.rst
diff --git a/docs/api/dtscalibration.plot_residuals_reference_sections_single.rst b/docs/api/dtscalibration.plot_residuals_reference_sections_single.rst
diff --git a/docs/api/dtscalibration.plot_sigma_report.rst b/docs/api/dtscalibration.plot_sigma_report.rst
diff --git a/docs/api/dtscalibration.read_apsensing_files.rst b/docs/api/dtscalibration.read_apsensing_files.rst
diff --git a/docs/api/dtscalibration.read_sensornet_files.rst b/docs/api/dtscalibration.read_sensornet_files.rst
diff --git a/docs/api/dtscalibration.read_sensortran_files.rst b/docs/api/dtscalibration.read_sensortran_files.rst
diff --git a/docs/api/dtscalibration.read_silixa_files.rst b/docs/api/dtscalibration.read_silixa_files.rst
diff --git a/docs/api/dtscalibration.shift_double_ended.rst b/docs/api/dtscalibration.shift_double_ended.rst
diff --git a/docs/api/dtscalibration.suggest_cable_shift_double_ended.rst b/docs/api/dtscalibration.suggest_cable_shift_double_ended.rst
diff --git a/docs/conf.py b/docs/conf.py
@@ -4,6 +4,7 @@
 
 
 extensions = [
+    "sphinx_rtd_theme",
     "sphinx.ext.autodoc",
     "sphinx.ext.autosummary",
     "sphinx.ext.coverage",

diff --git a/docs/index.rst b/docs/index.rst
@@ -3,11 +3,10 @@ Contents
 ========
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 3
 
    readme
    installation
-   usage
    learn_by_examples
    reference/index
    contributing

diff --git a/docs/notebooks/07Calibrate_single_ended.ipynb b/docs/notebooks/07Calibrate_single_ended.ipynb
@@ -52,7 +52,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Read the raw data files loaded from your DTS machine\n",
+    "## Read the raw data files loaded from your DTS machine\n",
     "Use `read_silixa_files` for reading files from a Silixa device. The following functions are available for reading files from other devices: `read_sensortran_files`, `read_apsensing_files`, and `read_sensornet_files`. See Notebook 1.\n",
     "\n",
     "Calibration is performed on sections that have a known"
@@ -79,7 +79,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Define the reference fiber sections that have a known temperature\n",
+    "## Define the reference fiber sections that have a known temperature\n",
     "As explained in Notebook 3. DTS devices come with temperature probes to measure the temperature of the water baths. These measurements are stored in the data that was loaded in the previous step and are loaded automatically. In the case you would like to use an external temperature sensor, have a look at notebook `09Import_timeseries` to append those measurements to the `ds` before continuing with the calibration. "
    ]
   },
@@ -100,7 +100,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Estimate the variance of the noise in the Stokes and anti-Stokes measurements\n",
+    "## Estimate the variance of the noise in the Stokes and anti-Stokes measurements\n",
     "First calculate the variance of the noise in the measured Stokes and anti-Stokes signals. See Notebook 4 for more information.\n",
     "\n",
     "The Stokes and anti-Stokes signals should follow a smooth decaying exponential. This function fits a decaying exponential to each reference section for each time step. The variance of the residuals between the measured Stokes and anti-Stokes signals and the fitted signals is used as an estimate of the variance in measured signals. This algorithm assumes that the temperature is the same for the entire section but may vary over time and differ per section."
@@ -143,7 +143,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Perform calibration and compute the temperature\n",
+    "## Perform calibration and compute the temperature\n",
     "We calibrate the measurements and their uncertainty with a single method call. The temperature is stored by default as the `ds.tmpf` dataarray and the variance of its approximation as `ds.tmpf_var`."
    ]
   },
@@ -167,7 +167,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Plot the temperature and uncertainty of the estimated temperature\n",
+    "## Plot the temperature and uncertainty of the estimated temperature\n",
     "First, the temperature for the entire fiber is plotted. Second, the temperature and its standard error are plotted for the first timestep."
    ]
   },

diff --git a/docs/notebooks/08Calibrate_double_ended.ipynb b/docs/notebooks/08Calibrate_double_ended.ipynb
@@ -56,7 +56,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Read the raw data files loaded from your DTS machine\n",
+    "## Read the raw data files loaded from your DTS machine\n",
     "Use `read_silixa_files` for reading files from a Silixa device. The following functions are available for reading files from other devices: `read_sensortran_files`, `read_apsensing_files`, and `read_sensornet_files`. See Notebook 1. If your DTS device was configured such that your forward- and backward measurements are stored in seperate folders have a look at `11Merge_single_measurements_into_double` example notebook. "
    ]
   },
@@ -77,7 +77,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Align measurements of the forward and backward channels"
+    "## Align measurements of the forward and backward channels"
    ]
   },
   {
@@ -147,7 +147,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Define the reference fiber sections that have a known temperature\n",
+    "## Define the reference fiber sections that have a known temperature\n",
     "As explained in Notebook 3. As explained in Notebook 3. DTS devices come with temperature probes to measure the temperature of the water baths. These measurements are stored in the data that was loaded in the previous step and are loaded automatically. In the case you would like to use an external temperature sensor, have a look at notebook `09Import_timeseries` to append those measurements to the `ds` before continuing with the calibration."
    ]
   },
@@ -167,7 +167,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Estimate the variance of the noise in the Stokes and anti-Stokes measurements\n",
+    "## Estimate the variance of the noise in the Stokes and anti-Stokes measurements\n",
     "First calculate the variance in the measured Stokes and anti-Stokes signals, in the forward and backward direction. See Notebook 4 for more information.\n",
     "\n",
     "The Stokes and anti-Stokes signals should follow a smooth decaying exponential. This function fits a decaying exponential to each reference section for each time step. The variance of the residuals between the measured Stokes and anti-Stokes signals and the fitted signals is used as an estimate of the variance in measured signals. This algorithm assumes that the temperature is the same for the entire section but may vary over time and differ per section."
@@ -219,7 +219,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Perform calibration and compute the temperature\n",
+    "## Perform calibration and compute the temperature\n",
     "We calibrate the measurements with a single method call. Three temperatures are estimated for double-ended setups. The temperature using the Stokes and anti-Stokes meassurements of the forward channel, `tmpf`. The temperature of the backward channel, `tmpb`. And the weigthed average of the two, `tmpw`. The latter is the best estimate of the temperature along the fiber with the smallest uncertainty."
    ]
   },
@@ -264,7 +264,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Uncertainty of the calibrated temperature\n",
+    "## Uncertainty of the calibrated temperature\n",
     "The uncertainty of the calibrated temperature can be computed in two manners:\n",
     "1. The variance of the calibrated temperature can be approximated using linear error propagation\n",
     "    - Very fast computation\n",

diff --git a/docs/notebooks/14Lossy_splices.ipynb b/docs/notebooks/14Lossy_splices.ipynb
@@ -24,7 +24,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Demonstration\n",
+    "## Demonstration\n",
     "To demonstrate the effect of a lossy splice, we'll load the same dataset that was used in previous notebooks, and modify the data to simulate a lossy splice."
    ]
   },
@@ -230,5 +230,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }
diff --git a/docs/notebooks/17Temperature_uncertainty_single_ended.ipynb b/docs/notebooks/17Temperature_uncertainty_single_ended.ipynb
@@ -5,7 +5,7 @@
    "id": "bcd29771",
    "metadata": {},
    "source": [
-    "# Uncertainty of the temperature estimated using single-ended calibration\n",
+    "# 17. Uncertainty of the temperature estimated using single-ended calibration\n",
     "After comleting single-ended calibration, you might be interested in inspecting the uncertainty of the estimated temperature.\n",
     "- Decomposing the uncertainty\n",
     "- Monte Carlo estimate of the standard error\n",

diff --git a/docs/reference/index.rst b/docs/reference/index.rst
@@ -5,5 +5,6 @@ Reference
     :glob:
 
 .. automodapi:: dtscalibration
-   :no-inheritance-diagram:
    :skip: plot_dask
+   :members:
+   :no-inheritance-diagram:
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,7 +1 @@
-IPython
-matplotlib>=3.0.0
-nbsphinx
-recommonmark
-sphinx<6
-sphinx-automodapi
 -e .[docs]
diff --git a/docs/usage.rst b/docs/usage.rst