Merge pull request #12 from jmbhughes/v1.0

V1.0

.github/workflows/ci.yaml

@@ -0,0 +1,45 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: CI
+
+on:
+  push:
+  pull_request:
+  schedule:
+    - cron: '0 8 * * *'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest pytest-cov hypothesis
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pip install .
+        pytest --cov
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v3
+      with:
+        fail_ci_if_error: true
+        verbose: true

requirements.txt

@@ -0,0 +1,13 @@
+pyqt5 >= 5.15.9
+matplotlib >= 3.7.2
+astropy >= 5.3.1
+numpy >= 1.25.1
+goes-solar-retriever >= 0.4.0
+scipy >= 1.11.1
+scikit-image >= 0.21.0
+pillow >= 10.0.0
+sunpy >= 5.0.0
+lxml >= 4.9.3
+reproject >= 0.11.0
+zeep >= 4.2.1
+drms >= 0.6.4

setup.py

@@ -11,7 +11,7 @@
     name='solarannotator',
     long_description=long_description,
     long_description_content_type='text/markdown',
-    version='0.3.1',
+    version='1.0.0',
     packages=['solarannotator'],
     url='',
     license='',

solarannotator/gui.py

@@ -2,7 +2,7 @@
 import PyQt5
 from PyQt5 import QtCore, QtWidgets
 from PyQt5.QtWidgets import QWidget, QLabel, QAction, QTabWidget, QPushButton, QFileDialog, QRadioButton, QMessageBox, \
-    QComboBox, QLineEdit, QSizePolicy
+    QComboBox, QLineEdit, QSizePolicy, QCheckBox
 from PyQt5.QtCore import QDateTime
 from PyQt5.QtGui import QIcon, QDoubleValidator
 from datetime import datetime, timedelta
@@ -18,6 +18,8 @@
 from matplotlib.backends.backend_qt5agg import FigureCanvas, NavigationToolbar2QT as NavigationToolbar
 from matplotlib.figure import Figure
 
+from solarannotator.template import create_thmap_template
+
 if hasattr(QtCore.Qt, 'AA_EnableHighDpiScaling'):
     PyQt5.QtWidgets.QApplication.setAttribute(QtCore.Qt.AA_EnableHighDpiScaling, True)
 
@@ -69,7 +71,7 @@ def __init__(self, config):
         self.pix = np.vstack((xv.flatten(), yv.flatten())).T
 
         lineprops = dict(color="red", linewidth=2)
-        self.lasso = LassoSelector(self.axs[0], self.onlasso, lineprops=lineprops)
+        self.lasso = LassoSelector(self.axs[0], self.onlasso, props=lineprops)
         self.fig.tight_layout()
 
     def onlasso(self, verts):
@@ -209,7 +211,7 @@ def clearBoundaries(self):
         self.region_patches = []
         self.fig.canvas.draw_idle()
 
-    def loadThematicMap(self, thmap):
+    def loadThematicMap(self, thmap, template=True):
         try:
             download_message = QMessageBox.information(self,
                                                        'Downloading',
@@ -220,9 +222,11 @@ def loadThematicMap(self, thmap):
             self.data_does_not_exist_popup()
         else:
             self.thmap = thmap
+            if template:
+                self.thmap = create_thmap_template(self.composites)
             self.thmap.copy_195_metadata(self.composites)
             self.history = [thmap.data.copy()]
-            self.thmap_data = thmap.data
+            self.thmap_data = self.thmap.data
             self.thmap_axesimage.set_data(self.thmap_data)
             self.preview_axesimage.set_data(self.composites['94'].data)
             self.fig.canvas.draw_idle()
@@ -479,9 +483,12 @@ def initUI(self):
         layout = QtWidgets.QHBoxLayout()
         instructions = QLabel("Please select a time for the new file.", self)
         self.dateEdit = QtWidgets.QDateTimeEdit(QDateTime.currentDateTime())
+        self.template_option = QCheckBox("Use template")
+        self.template_option.setChecked(True)
         submit_button = QPushButton("Submit")
         layout.addWidget(instructions)
         layout.addWidget(self.dateEdit)
+        layout.addWidget(self.template_option)
         layout.addWidget(submit_button)
         self.setLayout(layout)
         submit_button.clicked.connect(self.onSubmit)
@@ -493,7 +500,7 @@ def onSubmit(self):
                                 {'DATE-OBS': str(self.parent.date),
                                  'DATE': str(datetime.today())},
                                 self.parent.config.solar_class_name)
-        self.parent.annotator.loadThematicMap(new_thmap)
+        self.parent.annotator.loadThematicMap(new_thmap, self.template_option.isChecked())
         self.parent.controls.onTabChange()  # Us
         self.close()
         self.parent.setWindowTitle("SolarAnnotator: {}".format(new_thmap.date_obs))

solarannotator/io.py

@@ -11,7 +11,6 @@
 import sunpy.map
 from sunpy.coordinates import Helioprojective
 
-
 Image = namedtuple('Image', 'data header')
 
 
@@ -29,9 +28,9 @@ def retrieve(date):
     @staticmethod
     def _load_gong_image(date, suvi_195_image):
         # Find an image and download it
-        results = Fido.search(a.Time(date-timedelta(hours=1), date+timedelta(hours=1)),
+        results = Fido.search(a.Time(date - timedelta(hours=1), date + timedelta(hours=1)),
                               a.Wavelength(6563 * u.Angstrom), a.Source("GONG"))
-        selection = results[0][len(results[0])//2]  # only download the middle image
+        selection = results[0][len(results[0]) // 2]  # only download the middle image
         downloads = Fido.fetch(selection)
         with fits.open(downloads[0]) as hdul:
             gong_data = hdul[1].data
@@ -56,7 +55,6 @@ def _load_gong_image(date, suvi_195_image):
 
         return Image(out.data, dict(out.meta))
 
-
     @staticmethod
     def _load_suvi_composites(date):
         satellite = Satellite.GOES16
@@ -77,7 +75,6 @@ def _load_suvi_composites(date):
             os.remove(fn)
         return composites
 
-
     @staticmethod
     def create_empty():
         mapping = {"94": Image(np.zeros((1280, 1280)), {}),
@@ -95,6 +92,52 @@ def __getitem__(self, key):
     def channels(self):
         return list(self.images.keys())
 
+    def get_solar_radius(self, channel="304", refine=True):
+        """
+        Gets the solar radius from the header of the specified channel
+        :param channel: channel to get radius from
+        :param refine: whether to refine the metadata radius to better approximate the edge
+        :return: solar radius specified in the header
+        """
+
+        # Return the solar radius
+        if channel not in self.channels():
+            raise RuntimeError("Channel requested must be one of {}".format(self.channels()))
+        try:
+            solar_radius = self.images[channel].header['DIAM_SUN'] / 2
+            if refine:
+                composite_img = self.images[channel].data
+                # Determine image size
+                image_size = np.shape(composite_img)[0]
+                # Find center and radial mesh grid
+                center = (image_size / 2) - 0.5
+                xm, ym = np.meshgrid(np.linspace(0, image_size - 1, num=image_size),
+                                     np.linspace(0, image_size - 1, num=image_size))
+                xm_c = xm - center
+                ym_c = ym - center
+                rads = np.sqrt(xm_c ** 2 + ym_c ** 2)
+                # Iterate through radii within a range past the solar radius
+                accuracy = 15
+                rad_iterate = np.linspace(solar_radius, solar_radius + 50, num=accuracy)
+                img_avgs = []
+                for rad in rad_iterate:
+                    # Create a temporary solar image corresponding to the layer
+                    solar_layer = np.zeros((image_size, image_size))
+                    # Find indices in mask of the layer
+                    indx_layer = np.where(rad >= rads)
+                    # Set temporary image corresponding to indices to solar image values
+                    solar_layer[indx_layer] = composite_img[indx_layer]
+                    # Appends average to image averages
+                    img_avgs.append(np.mean(solar_layer))
+                # Find "drop off" where mask causes average image brightness to drop
+                diff_avgs = np.asarray(img_avgs[0:accuracy - 1]) - np.asarray(img_avgs[1:accuracy])
+                # Return the radius that best represents the edge of the sun
+                solar_radius = rad_iterate[np.where(np.amax(diff_avgs))[0] + 1]
+        except KeyError:
+            raise RuntimeError("Header does not include the solar diameter or radius")
+        else:
+            return solar_radius
+
 
 class ThematicMap:
     def __init__(self, data, metadata, theme_mapping):

solarannotator/template.py

@@ -0,0 +1,74 @@
+from solarannotator.io import ImageSet, ThematicMap
+from datetime import datetime, timedelta
+import numpy as np
+
+
+def create_mask(radius, image_size):
+    """
+    Inputs:
+        - Radius: Radius (pixels) within which a certain theme should be assigned
+        - Image size: tuple of (x, y) size (pixels) that represents size of image
+    """
+    # Define image center
+    center_x = (image_size[0] / 2) - 0.5
+    center_y = (image_size[1] / 2) - 0.5
+
+    # Create mesh grid of image coordinates
+    xm, ym = np.meshgrid(np.linspace(0, image_size[0] - 1, num=image_size[0]),
+                         np.linspace(0, image_size[1] - 1, num=image_size[1]))
+
+    # Center each mesh grid (zero at the center)
+    xm_c = xm - center_x
+    ym_c = ym - center_y
+
+    # Create array of radii
+    rad = np.sqrt(xm_c ** 2 + ym_c ** 2)
+
+    # Create empty mask of same size as the image
+    mask = np.zeros((image_size[0], image_size[1]))
+
+    # Apply the mask as true for anything within a radius
+    mask[(rad < radius)] = 1
+
+    # Return the mask
+    return mask.astype('bool')
+
+
+def create_thmap_template(image_set, limb_thickness=10):
+    """
+    Input: Image set object as input, and limb thickness in pixels
+    Output: thematic map object
+    Process:
+        - Get the solar radius with predefined function
+        - Create empty thematic map
+        - Define concentric layers separated by solar radius + limb thickness, and create thmap
+        - Return the thematic map object
+
+    Note copied from Alison Jarvis
+    """
+
+    # Get the solar radius with class function
+    solar_radius = image_set.get_solar_radius()
+
+    # Define end of disk and end of limb radii
+    disk_radius = solar_radius - (limb_thickness / 2)
+    limb_radius = solar_radius + (limb_thickness / 2)
+
+    # Create concentric layers for disk, limb, and outer space
+    # First template layer, outer space (value 1) with same size as composites
+    imagesize = np.shape(image_set['171'].data)
+    thmap_data = np.ones(imagesize)
+    # Mask out the limb (value 8)
+    limb_mask = create_mask(limb_radius, imagesize)
+    thmap_data[limb_mask] = 8
+    # Mask out the disk with quiet sun (value 7)
+    qs_mask = create_mask(disk_radius, imagesize)
+    thmap_data[qs_mask] = 7
+
+    # Create a thematic map object with this data and return it
+    theme_mapping = {1: 'outer_space', 3: 'bright_region', 4: 'filament', 5: 'prominence', 6: 'coronal_hole',
+                     7: 'quiet_sun', 8: 'limb', 9: 'flare'}
+    thmap_template = ThematicMap(thmap_data, {'DATE-OBS': image_set['171'].header['DATE-OBS']}, theme_mapping)
+
+    # Return the thematic map object
+    return thmap_template

tests/test_template.py

@@ -0,0 +1,7 @@
+from solarannotator.template import create_mask
+
+
+def test_mask_creation():
+    mask = create_mask(500, (2048, 2048))
+    assert not mask[0, 0]
+    assert mask[1024, 1024]