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pep8 fixes
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@bhilbert4
bhilbert4 committed Sep 28, 2023
1 parent 23d02e7 commit a22b9cc
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Showing 3 changed files with 20 additions and 38 deletions.
20 changes: 6 additions & 14 deletions jwql/instrument_monitors/common_monitors/dark_monitor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -275,14 +275,14 @@ def create_mean_slope_figure(self, image, num_files, hotxy=None, deadxy=None, no

# Create figure
start_time = Time(float(self.query_start), format='mjd').tt.datetime.strftime("%m/%d/%Y")
end_time = Time(float(self.query_end), format='mjd').tt.datetime.strftime("%m/%d/%Y")
end_time = Time(float(self.query_end), format='mjd').tt.datetime.strftime("%m/%d/%Y")

self.plot = figure(title=f'{self.aperture}: {num_files} files. {start_time} to {end_time}', tools='')
# tools='pan,box_zoom,reset,wheel_zoom,save')
self.plot.x_range.range_padding = self.plot.y_range.range_padding = 0

# Create the color mapper that will be used to scale the image
mapper = LinearColorMapper(palette='Viridis256', low=(img_med-5*img_dev) ,high=(img_med+5*img_dev))
mapper = LinearColorMapper(palette='Viridis256', low=(img_med - (5 * img_dev)), high=(img_med + (5 * img_dev)))

# Plot image and add color bar
imgplot = self.plot.image(image=[image], x=0, y=0, dw=nx, dh=ny,
Expand All @@ -291,13 +291,6 @@ def create_mean_slope_figure(self, image, num_files, hotxy=None, deadxy=None, no
color_bar = ColorBar(color_mapper=mapper, width=8, title='DN/sec')
self.plot.add_layout(color_bar, 'right')

# Add hover tool for all pixel values
#hover_tool = HoverTool(tooltips=[('(x, y):', '($x{int}, $y{int})'),
# ('value:', '@image')
# ],
# renderers=[imgplot])
#self.plot.tools.append(hover_tool)

if (('FULL' in self.aperture) or ('_CEN' in self.aperture)):

if hotxy is not None:
Expand Down Expand Up @@ -337,22 +330,21 @@ def create_mean_slope_figure(self, image, num_files, hotxy=None, deadxy=None, no
base_start = Time(float(base_parts[3]), format='mjd').tt.datetime
base_end = Time(float(base_parts[5]), format='mjd').tt.datetime
base_start_time = base_start.strftime("%m/%d/%Y")
base_end_time = base_end.strftime("%m/%d/%Y")
base_end_time = base_end.strftime("%m/%d/%Y")
legend_title = f'Compared to dark from {base_start_time} to {base_end_time}'
else:
legend_title = 'Compared to previous mean dark'
legend = Legend(items=[hot_legend, dead_legend, noisy_legend],
location="center",
orientation='vertical',
title = legend_title)
title=legend_title)

self.plot.add_layout(legend, 'below')

# Save the plot in a png
save_png(self.plot, filename=output_filename)
set_permissions(output_filename)


def get_metadata(self, filename):
"""Collect basic metadata from a fits file
Expand Down Expand Up @@ -650,14 +642,14 @@ def overplot_bad_pix(self, pix_type, coords, values):
sources[pix_type] = ColumnDataSource(data=dict(pixels_x=coords[0],
pixels_y=coords[1]
)
)
)

# Overplot the bad pixel locations
badpixplots[pix_type] = self.plot.circle(x=f'pixels_x', y=f'pixels_y',
source=sources[pix_type], color=colors[pix_type])

# Add to the legend
if numpix > 0:
if numpix > 0:
if numpix <= DARK_MONITOR_MAX_BADPOINTS_TO_PLOT:
text = f"{numpix} pix {adjective[pix_type]} than baseline"
else:
Expand Down
10 changes: 7 additions & 3 deletions jwql/utils/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -158,8 +158,7 @@ def create_png_from_fits(filename, outdir):
plot.ygrid.visible = False

# Create the color mapper that will be used to scale the image
#mapper = LogColorMapper(palette='Viridis256', low=(img_med-5*img_dev) ,high=(img_med+5*img_dev))
mapper = LogColorMapper(palette='Greys256', low=(img_med-5*img_dev) ,high=(img_med+5*img_dev))
mapper = LogColorMapper(palette='Greys256', low=(img_med - (5 * img_dev)),high=(img_med + (5 * img_dev)))

# Plot image
imgplot = plot.image(image=[image], x=0, y=0, dw=nx, dh=ny,
Expand All @@ -170,8 +169,13 @@ def create_png_from_fits(filename, outdir):
plot.yaxis.visible = False

# Save the plot in a png
<<<<<<< Updated upstream
output_filename = os.path.join(outdir, os.path.basename(filename).replace('fits','png'))
save_png(plot, filename=output_filename)
=======
output_filename = os.path.join(outdir, os.path.basename(filename).replace('fits', 'png'))
export_png(plot, filename=output_filename)
>>>>>>> Stashed changes
permissions.set_permissions(output_filename)
return output_filename
else:
Expand Down Expand Up @@ -750,7 +754,7 @@ def read_png(filename):

# Copy the RGBA image into view, flipping it so it comes right-side up
# with a lower-left origin
view[:,:,:] = np.flipud(np.asarray(rgba_img))
view[:, :, :] = np.flipud(np.asarray(rgba_img))
else:
view = None
# Return the 2D version
Expand Down
28 changes: 7 additions & 21 deletions jwql/website/apps/jwql/monitor_pages/monitor_bad_pixel_bokeh.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -74,8 +74,6 @@ def __init__(self, instrument):
# Get the relevant database tables
self.identify_tables()

#self.detectors = get_unique_values_per_column(self.pixel_table, 'detector')

self.detectors = sorted(DETECTOR_PER_INSTRUMENT[self.instrument])
if self.instrument == 'miri':
self.detectors = ['MIRIMAGE']
Expand Down Expand Up @@ -128,7 +126,6 @@ def modify_bokeh_saved_html(self):

self._html = "".join(newlines)


def run(self):

# Right now, the aperture name in the query history table is used as the title of the
Expand Down Expand Up @@ -163,7 +160,7 @@ def run(self):
# Insert into our html template and save
template_dir = os.path.join(os.path.dirname(__file__), '../templates')
template_file = os.path.join(template_dir, 'bad_pixel_monitor_savefile_basic.html')
temp_vars = {'inst': self.instrument, 'plot_script': script, 'plot_div':div}
temp_vars = {'inst': self.instrument, 'plot_script': script, 'plot_div': div}
self._html = file_html(tabs, CDN, f'{self.instrument} bad pix monitor', template_file, temp_vars)

# Modify the html such that our Django-related lines are kept in place,
Expand Down Expand Up @@ -264,7 +261,6 @@ def __init__(self, pixel_table, instrument, detector):
for badtype in self.badtypes:
self.get_trending_data(badtype)


def get_most_recent_entry(self):
"""Get all nedded data from the database tables.
"""
Expand Down Expand Up @@ -312,7 +308,7 @@ def get_trending_data(self, badpix_type):
# Query database for all data in the table with a matching detector and bad pixel type
all_entries_by_type = session.query(self.pixel_table.type, self.pixel_table.detector, func.array_length(self.pixel_table.x_coord, 1),
self.pixel_table.obs_mid_time) \
.filter(and_(self.pixel_table.detector == self.detector, self.pixel_table.type == badpix_type)) \
.filter(and_(self.pixel_table.detector == self.detector, self.pixel_table.type == badpix_type)) \
.all()

# Organize the results
Expand Down Expand Up @@ -463,7 +459,7 @@ def create_plot(self):
self.plot = figure(title=title_text, tools=tools,
x_axis_label="Pixel Number", y_axis_label="Pixel Number")
else:
self.plot = figure(tools='') #, x_axis_label="Pixel Number", y_axis_label="Pixel Number")
self.plot = figure(tools='')
self.plot.toolbar.logo = None
self.plot.toolbar_location = None
self.plot.min_border = 0
Expand All @@ -475,18 +471,9 @@ def create_plot(self):
# Plot image
if image is not None:
ny, nx = image.shape
#imgplot = self.plot.image(image=[image], x=0, y=0, dw=nx, dh=ny, color_mapper=mapper, level="image")



# Shift the figure title slightly right in this case to get it
# to align with the axes
#self.plot = figure(title=title, x_range=(0, self._detlen), y_range=(0, self._detlen), width=xdim, height=ydim*,
# tools='pan,box_zoom,reset,wheel_zoom,save', x_axis_label="Pixel Number", y_axis_label="Pixel Number")
self.plot.image_rgba(image=[image], x=0, y=0, dw=self._detlen, dh=self._detlen, alpha=0.5)



else:
# If the background image is not present, manually set the x and y range
self.plot.x_range.start = 0
Expand All @@ -511,11 +498,10 @@ def create_plot(self):
legend = Legend(items=[plot_legend],
location="center",
orientation='vertical',
title = legend_title)
title=legend_title)

self.plot.add_layout(legend, 'below')


def overplot_bad_pix(self):
"""Add a scatter plot of potential new bad pixels to the plot
Expand All @@ -537,7 +523,7 @@ def overplot_bad_pix(self):
# If there are no new bad pixels, write text within the figure mentioning that
txt_source = ColumnDataSource(data=dict(x=[self._detlen / 10], y=[self._detlen / 2],
text=[f'No new {self.badpix_type} pixels found']))
glyph = Text(x="x", y="y", text="text", angle=0., text_color="navy", text_font_size={'value':'20px'})
glyph = Text(x="x", y="y", text="text", angle=0., text_color="navy", text_font_size={'value': '20px'})
self.plot.add_glyph(txt_source, glyph)

# Insert a fake one, in order to get the plot to be made
Expand Down Expand Up @@ -668,7 +654,7 @@ def create_plot(self):
string_time=string_times,
value=[self.badpix_type] * len(self.num_pix)
)
)
)

self.plot = figure(title=f'{self.detector}: New {self.badpix_type} Pixels', tools='pan,box_zoom,reset,wheel_zoom,save',
background_fill_color="#fafafa")
Expand Down Expand Up @@ -696,7 +682,7 @@ def create_plot(self):
time_pad = datetime.timedelta(days=1)
self.plot.x_range.start = min(self.time) - time_pad
self.plot.x_range.end = max(self.time) + time_pad
self.plot.grid.grid_line_color="white"
self.plot.grid.grid_line_color = "white"
self.plot.xaxis.axis_label = 'Date'
self.plot.yaxis.axis_label = f'Number of {self.badpix_type} pixels'

Expand Down

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