def test_load_from_stream(self):
with open(osp.join(TEST_DIR, 'Starshot-30-deg-perfect.dcm'),
'rb') as f:
s = io.BytesIO(f.read())
star = Starshot(s)
star.analyze()
self.assertIsInstance(star, Starshot)
def construct_star(cls):
filename = cls.get_filename()
if cls.is_dir:
files = [osp.join(filename, file) for file in os.listdir(filename)]
star = Starshot.from_multiple_images(files, **cls.kwargs)
else:
star = Starshot(filename, **cls.kwargs)
return star
def run_star(path):
"""Function to pass to the process pool executor to process starshot images."""
try:
mystar = Starshot(path, sid=1000)
mystar.analyze()
if mystar.wobble.diameter_mm > 3:
raise Exception("Diamater was > 3mm.")
return 'Success'
except Exception as e:
return 'Failure: {} @ {}'.format(e, path)
def run_star(path):
"""Function to pass to the process pool executor to process starshot images."""
try:
mystar = Starshot(path, sid=1000)
mystar.analyze()
if mystar.wobble.diameter_mm > 3:
raise Exception("Diamater was > 3mm.")
return 'Success'
except Exception as e:
return 'Failure: {} @ {}'.format(e, path)
def setUpClass(cls):
img_dir = osp.join(TEST_DIR, 'set')
img_files = [
osp.join(img_dir, filename) for filename in os.listdir(img_dir)
]
cls.star = Starshot.from_multiple_images(img_files)
cls.star.analyze(radius=0.8)
def test_image_inverted(self):
"""Check that the demo image was actually inverted, as it needs to be."""
star = Starshot.from_demo_image()
top_left_corner_val_before = star.image.array[0, 0]
star._check_image_inversion()
top_left_corner_val_after = star.image.array[0, 0]
self.assertNotEqual(top_left_corner_val_before, top_left_corner_val_after)
def test_image_inverted(self):
"""Check that the demo image was actually inverted, as it needs to be."""
star = Starshot.from_demo_image()
top_left_corner_val_before = star.image.array[0, 0]
star.image.check_inversion_by_histogram(percentiles=[4, 50, 96])
top_left_corner_val_after = star.image.array[0, 0]
self.assertNotEqual(top_left_corner_val_before, top_left_corner_val_after)
def construct_star(cls):
filename = cls.get_filename()
if cls.is_dir:
files = [osp.join(filename, file) for file in os.listdir(filename)]
star = Starshot.from_multiple_images(files, **cls.kwargs)
else:
star = Starshot(filename, **cls.kwargs)
return star
def setUp(self):
self.star = Starshot.from_demo_image()
self.star.analyze()
def test_loading_from_zip(self):
img_zip = get_file_from_cloud_test_repo(['Starshot', 'set.zip'])
star = Starshot.from_zip(img_zip)
# shouldn't raise
star.analyze()
def starshot_helperf(args):
imgtype = args["imgtype"]
w = args["w"]
clip_box = args["clip_box"]
radius = args["radius"]
min_peak_height = args["min_peak_height"]
start_x = args["start_x"]
start_y = args["start_y"]
dpi = args["dpi"]
sid = args["sid"]
fwhm = args["fwhm"]
recursive = args["recursive"]
invert = args["invert"]
temp_folder = args["temp_folder"]
file_path = args["file_path"]
imgdescription = args["imgdescription"]
station = args["station"]
displayname = args["displayname"]
acquisition_datetime = args["acquisition_datetime"]
general_functions.set_configuration(args["config"])
# Collect data for "save results"
dicomenergy = general_functions.get_energy_from_imgdescription(imgdescription)
user_machine, user_energy = general_functions.get_user_machine_and_energy(station, dicomenergy)
machines_and_energies = general_functions.get_machines_and_energies(general_functions.get_treatmentunits_starshot())
tolerances = general_functions.get_tolerance_user_machine_starshot(user_machine) # If user_machne has specific tolerance
if not tolerances:
tolerance, pdf_report_enable = general_functions.get_settings_starshot()
else:
tolerance, pdf_report_enable = tolerances[0]
tolerance = float(tolerance) # If more than this, the test is "borderline", but not "failed"
save_results = {
"user_machine": user_machine,
"user_energy": user_energy,
"machines_and_energies": machines_and_energies,
"testtype": ["Collimator", "Couch", "Gantry"],
"displayname": displayname
}
if start_x==0 or start_y==0:
start_point=None
else:
start_point=(start_x, start_y)
if sid==0.0 and dpi==0:
try:
star = Starshot(file_path)
except Exception as e:
return template("error_template", {"error_message": "The Starshot module cannot calculate. "+str(e)})
elif sid==0.0 and dpi!=0:
try:
star = Starshot(file_path, dpi=dpi)
except Exception as e:
return template("error_template", {"error_message": "The Starshot module cannot calculate. "+str(e)})
elif sid!=0.0 and dpi==0:
try:
star = Starshot(file_path, sid=sid)
except Exception as e:
return template("error_template", {"error_message": "The Starshot module cannot calculate. "+str(e)})
else:
try:
star = Starshot(file_path, dpi=dpi, sid=sid)
except Exception as e:
return template("error_template", {"error_message": "The Starshot module cannot calculate. "+str(e)})
# Here we force pixels to background outside of box:
if clip_box != 0:
try:
star.image.check_inversion_by_histogram(percentiles=[4, 50, 96]) # Check inversion otherwise this might not work
general_functions.clip_around_image(star.image, clip_box)
except Exception as e:
return template("error_template", {"error_message": "Unable to apply clipbox. "+str(e)})
# If inversion is selected:
if invert:
star.image.invert()
# Now we try to analyse
try:
star.analyze(radius=radius, min_peak_height=min_peak_height, tolerance=tolerance,
start_point=start_point, fwhm=fwhm, recursive=recursive)
except Exception as e:
return template("error_template", {"error_message": "Module Starshot cannot calculate. "+str(e)})
fig_ss = Figure(figsize=(10, 6), tight_layout={"w_pad":4})
img_ax = fig_ss.add_subplot(1,2,1)
wobble_ax = fig_ss.add_subplot(1,2,2)
img_ax.imshow(star.image.array, cmap=matplotlib.cm.gray, interpolation="none", aspect="equal", origin='upper')
star.lines.plot(img_ax)
star.wobble.plot2axes(img_ax, edgecolor='green')
star.circle_profile.plot2axes(img_ax, edgecolor='green')
img_ax.axis('off')
img_ax.autoscale(tight=True)
img_ax.set_aspect(1)
img_ax.set_xticks([])
img_ax.set_yticks([])
star.lines.plot(wobble_ax)
star.wobble.plot2axes(wobble_ax, edgecolor='green')
star.circle_profile.plot2axes(wobble_ax, edgecolor='green')
wobble_ax.axis('off')
xlims = [star.wobble.center.x + star.wobble.diameter, star.wobble.center.x - star.wobble.diameter]
ylims = [star.wobble.center.y + star.wobble.diameter, star.wobble.center.y - star.wobble.diameter]
wobble_ax.set_xlim(xlims)
wobble_ax.set_ylim(ylims)
wobble_ax.axis('on')
wobble_ax.set_aspect(1)
script = mpld3.fig_to_html(fig_ss, d3_url=D3_URL, mpld3_url=MPLD3_URL)
variables = {
"script": script,
"passed": star.passed,
"radius": star.wobble.radius_mm,
"tolerance": star.tolerance,
"circle_center": star.wobble.center,
"pdf_report_enable": pdf_report_enable,
"save_results": save_results,
"acquisition_datetime": acquisition_datetime
}
# Generate pylinac report:
if pdf_report_enable == "True":
pdf_file = tempfile.NamedTemporaryFile(delete=False, prefix="Starshot_", suffix=".pdf", dir=config.PDF_REPORT_FOLDER)
if imgtype == "dicom":
metadata = RestToolbox.GetInstances(config.ORTHANC_URL, [w])
try:
patient = metadata[0]["PatientName"]
except:
patient = ""
try:
stationname = metadata[0]["StationName"]
except:
stationname = ""
try:
date_time = RestToolbox.get_datetime(metadata[0])
date_var = datetime.datetime.strptime(date_time[0], "%Y%m%d").strftime("%d/%m/%Y")
except:
date_var = ""
star.publish_pdf(pdf_file, notes=["Date = "+date_var, "Patient = "+patient, "Station = "+stationname])
else:
star.publish_pdf(pdf_file)
variables["pdf_report_filename"] = os.path.basename(pdf_file.name)
general_functions.delete_figure([fig_ss])
general_functions.delete_files_in_subfolders([temp_folder]) # Delete image
return template("starshot_results", variables)
def test_no_dpi(self):
# raise error when DPI isn't in image or given
with self.assertRaises(ValueError):
Starshot.from_url(self.real_url)
# but is fine when DPI is given
Starshot.from_url(self.real_url, **self.kwargs)
def setUpClass(cls):
img_dir = osp.join(TEST_DIR, 'set')
img_files = [osp.join(img_dir, filename) for filename in os.listdir(img_dir)]
cls.star = Starshot.from_multiple_images(img_files)
cls.star.analyze(radius=0.8)
def test_fails_with_tight_tol(self):
star = Starshot.from_demo_image()
star.analyze(tolerance=0.1)
self.assertFalse(star.passed)
def construct_star(cls):
return Starshot.from_demo_image()
def construct_star(cls):
return Starshot.from_demo_image()
def setUp(self):
self.star = Starshot.from_demo_image()
self.star.analyze()
def test_no_dpi(self):
# raise error when DPI isn't in image or given
with self.assertRaises(ValueError):
Starshot.from_url(self.full_url)
# but is fine when DPI is given
Starshot.from_url(self.full_url, **self.kwargs)
def test_load_from_file_object(self):
with open(osp.join(TEST_DIR, 'Starshot-30-deg-perfect.dcm'),
'rb') as f:
star = Starshot(f)
star.analyze()
self.assertIsInstance(star, Starshot)
def test_fails_with_tight_tol(self):
star = Starshot.from_demo_image()
star.analyze(tolerance=0.1)
self.assertFalse(star.passed)
def test_loading_from_zip(self):
img_zip = osp.join(TEST_DIR, 'set.zip')
star = Starshot.from_zip(img_zip)
# shouldn't raise
star.analyze()