dkist-processing-visp 3.3.0__py3-none-any.whl → 5.1.1__py3-none-any.whl

dkist_processing_visp-5.1.1.dist-info/RECORD

@@ -0,0 +1,94 @@
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docs/conf.py

@@ -1,4 +1,5 @@
 """Configuration file for the Sphinx documentation builder."""
+
 # -- stdlib imports ------------------------------------------------------------
 import importlib
 import sys
@@ -32,7 +33,10 @@ autoapi_dirs = [Path(package.__file__).parent]
 # autoapi_keep_files = True
 
 # -- Options for intersphinx extension -----------------------------------------
-intersphinx_mapping = create_intersphinx_mapping(repo_name)
+intersphinx_mapping = create_intersphinx_mapping(repo_name) | {
+    "lmfit": ("https://lmfit.github.io/lmfit-py", None),
+    "sklearn": ("https://scikit-learn.org/stable/", None),
+}
 # Remaining sphinx settings are in dkist-sphinx-theme conf.py
 
 # -- Project information -------------------------------------------------------

docs/gain_correction.rst

@@ -4,8 +4,8 @@ Gain Calibration
 Introduction
 ------------
 
-NOTE: The usage of the term "gain" throughout this document refers to total system response of the DKIST/ViSP optical
-train; it does NOT refer to the detector gain that has units of ADU / electron. Sometimes the term "flat" is used in
+NOTE: The usage of the term "gain" throughout this document refers to the total system response of the DKIST/ViSP optical
+train; it does NOT refer to the detector gain that has units of ADU / electron. Often the term "flat" is used in
 a way that is interchangeable with the usage of "gain" in this document.
 
 The ViSP gain calibration is broken down into the following steps across two pipeline tasks
@@ -13,20 +13,21 @@ The ViSP gain calibration is broken down into the following steps across two pip
 
 #. Subtract dark and :doc:`background <background_light>` signals from all input gain images.
 
-#. Compute an average, equalized lamp gain and mask the hairlines.
+#. Compute an average lamp gain and mask the hairlines.
 
-#. Divide the solar gain by the resulting lamp image and correct for :doc:`geometric </geometric>` rotation/shifts and
+#. Divide the solar gain by the resulting lamp image and correct for :doc:`geometric </geometric>` rotation and
    spectral curvature.
 
-#. Mask hairlines and compute 2D characteristic solar spectra with spatial median filter.
+#. Separate the true solar spectrum from vignetting effects by fitting a solar atlas to the solar gain data.
 
-#. Re-curve/shift/rotate the characteristic spectra into the same coordinates as the input frames.
+#. Mask hairlines and compute a 2D characteristic solar spectra with a spatial median filter over the vignette-corrected solar gain data.
+
+#. Re-curve and rotate the characteristic spectra into the same coordinates as the input frames.
 
 #. Remove the characteristic spectra from solar gain images that have NOT had a lamp correction applied.
 
-The result is a final gain image that can be applied to science data. Note that all steps happen separately for every
-modulator state and beam. This is because the geometric x/y shifts have been found to be significantly different for each
-modulator state and beam.
+The result is a final gain image that can be applied to science data. Note that all steps happen separately for each
+beam to capture the differences in optical response between the two beams.
 
 Important Features
 ------------------
@@ -49,40 +50,53 @@ from all input frames.
 Average Lamp Frames and Mask Hairlines
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-All lamp frames for a particular modulator state and beam are averaged into a single array. The slit hairlines are then
-identified by smoothing the image in the spatial dimension and then computing the relative difference between this smoothed
-image and the original image. Any pixels that deviate by a large amount (set by the ``hairline_fraction`` parameter) are
-considered to be hairline pixels. These hairline pixels are masked by replacing them with values from the smoothed array.
-
-Lamp gains for all modulator states are then compared and equalized so each individual modulator state has the same
-median as the median of all (pre-equalized) modulator states. This step helps to mitigate any residual polarization that
-may exist in input gain images that would otherwise affect the residual continuum polarization in the processed
-science frames.
-
-Finally, all lamp gain images have any spatial intensity gradients removed by normalizing each spatial position by its
-median. This removes known gradients caused by the different input illumination of the lamp compared to the Sun.
+All lamp frames for a single beam are averaged into a single array. The slit hairlines are then identified by smoothing
+the image in the spatial dimension and then computing the relative difference between this smoothed image and the
+original image. Any pixels that deviate by a large amount (set by the ``hairline_fraction`` parameter) are considered to
+be hairline pixels. These hairline pixels are masked by replacing them with values from the smoothed array.
 
 Prepare and Rectify Solar Frames
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-The averaged modulated lamp frames from the previous step are applied to dark/background subtracted solar gain frames through
-division. Then the pre-computed :doc:`geometric </geometric>` correction removes any spectral rotation, x/y shifts, and
-spectral curvature (in that order). At the end of this step the dispersion axis will be parallel to a pixel axis and a
-single spectral pixel will have the same physical wavelength value for all spatial pixels.
+The averaged lamp frames from the previous step are applied to dark/background subtracted solar gain frames through
+division. Then the pre-computed :doc:`geometric </geometric>` correction removes any spectral rotation and spectral
+curvature (in that order). Note that at this point we do NOT correct for X/Y offsets for two reasons: 1). a separate gain
+is computed for each beam so applying the beam offsets is not necessary, and 2). it has been found that the
+modstate-to-modstate offsets are small enough to ignore when making gain frames. At the end of this step the dispersion
+axis will be parallel to a pixel axis and a single spectral pixel will have the same physical wavelength value for all
+spatial pixels.
+
+Separate Solar and Vignette Signals
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Aperture masks in ViSP cause known vignetting in both the spatial and spectral dimensions and we need to capture this
+vignetting in our final gain images so it can be correctly removed from science data. To separate the spectral vignette
+signature from the true solar spectrum we fit a representative spectrum to a solar atlas with a parameterized continuum.
+The representative spectrum is a spatial median of the rectified solar gain array, and the continuum is parameterized as
+a polynomial with an order set by the ``solar_vignette_initial_continuum_poly_fit_order`` parameter. Atlas fits are
+done with the `solar-wavelength-calibration <https://docs.dkist.nso.edu/projects/solar-wavelength-calibration/en/latest/>`_
+package. We take the fit continuum as a first estimate of the vignette signal in the spectral dimension.
+
+This first vignette estimate is then removed from the representative spectrum, thus producing an estimate of the true
+solar signal, and that spectrum is divided from every spatial pixel of the gain array. The residuals capture how the
+vignette signal varies with spatial and spectral position across the chip. We fit these residuals for each spatial pixel
+to compute a fully 2D estimate of the true vignette signal. The order of this polynomial fit is set by the
+``solar_vignette_spectral_poly_fit_order`` parameter.
 
 Compute Characteristic Spectra
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-First, the slit hairlines are masked using the same method as :ref:`above <hairline-description>`.
+First, the 2D vignette signal is divided from the solar gain array and the slit hairlines are masked using the same
+method as :ref:`above <hairline-description>`.
 
 The goal of this step is to derive pure solar spectra, free from any optical effects of the DKIST/ViSP system. By applying
-lamp gain frames to our solar images we have already removed a lot of optical effects, but some spatial variations still
-remain. Thus, the characteristic spectra is computed by applying a median filter (with width controlled by the
-``solar_spectral_avg_window`` parameter) in the spatial direction. Previously, a single, median spectrum had been used,
-but it did not accurately capture small, but important variations in spectral shape along the slit.
+lamp gain and vignette corrections to our solar images we have already removed a lot of optical effects, but some spatial
+variations still remain. Thus, the characteristic spectra is computed by applying a median filter (with width controlled
+by the ``solar_spatial_median_filter_width_px`` parameter) in the spatial direction. Previously, a single, median spectrum had been
+used, but it did not accurately capture small, but important variations in spectral shape along the slit.
 
-Finally, the smooth characteristic spectra has any spatial gradients removed by normalizing each spatial positions by its
-median. This ensures that the characteristic spectra contain *only* pure solar spectra, and thus any real spatial
+Finally, the smooth characteristic spectra have any spatial gradients removed by normalizing each spatial position by its
+continuum level. This ensures that the characteristic spectra contain *only* pure solar spectra, and thus any real spatial
 gradients are preserved in the final gain image. This normalization also ensures the absolute flux of the final
 gain images is preserved so that science frames will have values relative to average disk center (where the solar images
 are taken).
@@ -90,21 +104,15 @@ are taken).
 Un-rectify Characteristic Spectra
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-The characteristic spectra have spectral shifts, x/y offsets, and spectral rotation re-applied to bring them back into
-raw input pixel coordinates.
-
-The spectral curvature is NOT applied using the precomputed curvature. Instead, for each spatial position a new spectral
-shift is computed that minimizes the residual of the final gain image at that position. This step is needed because the
-characteristic spectra have *slightly* different spectral shapes than the input solar image (see above) and any small
-misalignment causes large, sharp residuals in the line wings. By explicitly minimizing final gain residuals we ensure
-that the new spectral shifts remove the solar signal as much as possible.
+The characteristic spectra have spectral shifts and spectral rotation re-applied to bring them back into raw input pixel
+coordinates.
 
 Remove Characteristic Solar Spectra from Input Solar Frames
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The dark/background corrected solar gain image is simply divided by the re-distorted characteristic spectra. Because we
-do NOT use a solar image with a lamp correction applied, the resulting gain image includes the full optical response of
-the system and can be applied directly to the science data.
+do NOT use a solar image with a lamp or vignette correction applied, the resulting gain image includes the full optical
+response of the system and can be applied directly to the science data.
 
 As mentioned above, these gain calibration images are not normalized. The result is that L1 science data will have
 values that are relative to solar disk center (where the solar gain images are observed).

dkist_processing_visp/tasks/mixin/line_zones.py

@@ -1,115 +0,0 @@
-"""Helper functions for line zone determination."""
-import numpy as np
-import peakutils
-import scipy.signal as sps
-from dkist_service_configuration.logging import logger
-
-
-class LineZonesMixin:
-    """Helper functions for line zone determination."""
-
-    def compute_line_zones(
-        self,
-        spec_2d: np.ndarray,
-        prominence: float = 0.2,
-        width: float = 2,
-        bg_order: int = 22,
-        normalization_percentile: int = 99,
-        rel_height=0.97,
-    ) -> list[tuple[int, int]]:
-        """
-        Identify spectral regions around strong spectra features.
-
-        Parameters
-        ----------
-        spec_2d : np.ndarray
-            Data
-
-        prominence : float
-            Zone prominence threshold used to identify strong spectral features
-
-        width : float
-            Zone width
-
-        bg_order : int
-            Order of polynomial fit used to remove continuum when identifying strong spectral features
-
-        normalization_percentile : int
-            Compute this percentile of the data along a specified axis
-
-
-
-        Returns
-        -------
-        List
-            List of regions to remove
-
-        """
-        logger.info(
-            f"Finding zones using {prominence=}, {width=}, {bg_order=}, {normalization_percentile=}, and {rel_height=}"
-        )
-        # Compute average along slit to improve signal. Line smearing isn't important here
-        avg_1d = np.mean(spec_2d, axis=1)
-
-        # Convert to an emission spectrum and remove baseline continuum so peakutils has an easier time
-        em_spec = -1 * avg_1d + avg_1d.max()
-        em_spec /= np.nanpercentile(em_spec, normalization_percentile)
-        baseline = peakutils.baseline(em_spec, bg_order)
-        em_spec -= baseline
-
-        # Find indices of peaks
-        peak_idxs = sps.find_peaks(em_spec, prominence=prominence, width=width)[0]
-
-        # Find the rough width based only on the height of the peak
-        #  rips and lips are the right and left borders of the region around the peak
-        _, _, rips, lips = sps.peak_widths(em_spec, peak_idxs, rel_height=rel_height)
-
-        # Convert to ints so they can be used as indices
-        rips = np.floor(rips).astype(int)
-        lips = np.ceil(lips).astype(int)
-
-        # Remove any regions that are contained within another region
-        ranges_to_remove = self.identify_overlapping_zones(rips, lips)
-        rips = np.delete(rips, ranges_to_remove)
-        lips = np.delete(lips, ranges_to_remove)
-
-        return list(zip(rips, lips))
-
-    @staticmethod
-    def identify_overlapping_zones(rips: np.ndarray, lips: np.ndarray) -> list[int]:
-        """
-        Identify line zones that overlap with other zones. Any overlap greater than 1 pixel is flagged.
-
-        Parameters
-        ----------
-        rips : np.ndarray
-            Right borders of the region around the peak
-
-        lips : np.ndarray
-            Left borders of the region around the peak
-
-        Returns
-        -------
-        List
-            List of ranges to be removed
-        """
-        all_ranges = [np.arange(zmin, zmax) for zmin, zmax in zip(rips, lips)]
-        ranges_to_remove = []
-        for i in range(len(all_ranges)):
-            target_range = all_ranges[i]
-            for j in range(i + 1, len(all_ranges)):
-                if (
-                    np.intersect1d(target_range, all_ranges[j]).size > 1
-                ):  # Allow for a single overlap just to be nice
-                    if target_range.size > all_ranges[j].size:
-                        ranges_to_remove.append(j)
-                        logger.info(
-                            f"Zone ({all_ranges[j][0]}, {all_ranges[j][-1]}) inside zone ({target_range[0]}, {target_range[-1]})"
-                        )
-                    else:
-                        ranges_to_remove.append(i)
-                        logger.info(
-                            f"Zone ({target_range[0]}, {target_range[-1]}) inside zone ({all_ranges[j][0]}, {all_ranges[j][-1]})"
-                        )
-
-        return ranges_to_remove