def test_imageWriterCreatesCorrectFile(self):
writer = NrrdWriter(self.msi)
writer.write(self.fileUriToWrite)
reader = NrrdReader()
msi = reader.read(self.fileUriToWrite)
self.assertTrue(msi == helpers.getFakeMsi(),
"image correctly written and read")
def test_imageWriterCreatesCorrectFile(self):
writer = NrrdWriter(self.msi)
writer.write(self.fileUriToWrite)
reader = NrrdReader()
msi = reader.read(self.fileUriToWrite)
self.assertTrue(msi == helpers.getFakeMsi(),
"image correctly written and read")
def test_write_one_d_image_works(self):
writer = NrrdWriter(self.msi)
msimani.calculate_mean_spectrum(self.msi)
writer.write(self.fileUriToWrite)
reader = NrrdReader()
msi = reader.read(self.fileUriToWrite)
np.testing.assert_array_equal(msi.get_image(),
np.array([1, 2, 3, 4, 5]),
"1d image correctly written and read")
def test_write_one_d_image_works(self):
writer = NrrdWriter(self.msi)
msimani.calculate_mean_spectrum(self.msi)
writer.write(self.fileUriToWrite)
reader = NrrdReader()
msi = reader.read(self.fileUriToWrite)
np.testing.assert_array_equal(msi.get_image(),
np.array([1, 2, 3, 4, 5]),
"1d image correctly written and read")
class TestNrrdReader(unittest.TestCase):
def setUp(self):
self.nrrdReader = NrrdReader()
self.msi = self.nrrdReader.read('./msi/data/testMsi.nrrd')
def test_read_does_not_crash(self):
# if we got this far, at least an image was read.
self.assertTrue(len(self.msi.get_image().shape) == 3,
"read image has correct basic shape dimensions")
self.assertTrue(self.msi.get_image().shape[-1] == 5,
"read image has correct number of image stacks")
self.assertTrue(np.array_equal(self.msi.get_image()[2, 2, :],
np.array([1, 2, 3, 4, 5])),
"read image contains correct data")
def test_read_non_existing_image_returns_exception(self):
with self.assertRaises(RuntimeError):
self.nrrdReader.read("./msi/data/asdf.nrrd")
class TestNrrdReader(unittest.TestCase):
def setUp(self):
self.nrrdReader = NrrdReader()
self.msi = self.nrrdReader.read('./msi/data/testMsi.nrrd')
def test_read_does_not_crash(self):
# if we got this far, at least an image was read.
self.assertTrue(len(self.msi.get_image().shape) == 3,
"read image has correct basic shape dimensions")
self.assertTrue(self.msi.get_image().shape[-1] == 5,
"read image has correct number of image stacks")
self.assertTrue(np.array_equal(self.msi.get_image()[2, 2, :],
np.array([1, 2, 3, 4, 5])),
"read image contains correct data")
def test_read_non_existing_image_returns_exception(self):
with self.assertRaises(RuntimeError):
self.nrrdReader.read("./msi/data/asdf.nrrd")
def run(self):
nrrd_reader = NrrdReader()
tiff_ring_reader = TiffRingReader()
# read the flatfield
flat = nrrd_reader.read(self.input()[1].path)
dark = nrrd_reader.read(self.input()[3].path)
# read the msi
nr_filters = len(sc.other["RECORDED_WAVELENGTHS"])
msi, segmentation = tiff_ring_reader.read(self.input()[2].path,
nr_filters)
# only take into account not saturated pixels.
segmentation = np.logical_and(segmentation,
(np.max(msi.get_image(),
axis=-1) < 1000.))
# read the regressor
e_file = open(self.input()[0].path, 'r')
e = pickle.load(e_file)
# correct image setup
filter_nr = int(self.image_name[-6:-5])
original_order = np.arange(nr_filters)
new_image_order = np.concatenate((
original_order[nr_filters - filter_nr:],
original_order[:nr_filters - filter_nr]))
# resort msi to restore original order
msimani.get_bands(msi, new_image_order)
# correct by flatfield
msimani.image_correction(msi, flat, dark)
# create artificial rgb
rgb_image = msi.get_image()[:, :, [2, 3, 1]]
rgb_image /= np.max(rgb_image)
rgb_image *= 255.
# preprocess the image
# sortout unwanted bands
print "1"
# zero values would lead to infinity logarithm, thus clip.
msi.set_image(np.clip(msi.get_image(), 0.00001, 2. ** 64))
# normalize to get rid of lighting intensity
norm.standard_normalizer.normalize(msi)
# transform to absorption
msi.set_image(-np.log(msi.get_image()))
# normalize by l2 for stability
norm.standard_normalizer.normalize(msi, "l2")
print "2"
# estimate
sitk_image, time = estimate_image(msi, e)
image = sitk.GetArrayFromImage(sitk_image)
plt.figure()
print "3"
rgb_image = rgb_image.astype(np.uint8)
im = Image.fromarray(rgb_image, 'RGB')
enh_brightness = ImageEnhance.Brightness(im)
im = enh_brightness.enhance(10.)
plotted_image = np.array(im)
top_left_axis = plt.gca()
top_left_axis.imshow(plotted_image, interpolation='nearest')
top_left_axis.xaxis.set_visible(False)
top_left_axis.yaxis.set_visible(False)
plt.set_cmap("jet")
print "4"
# plot parametric maps
segmentation[0, 0] = 1
segmentation[0, 1] = 1
oxy_image = np.ma.masked_array(image[:, :, 0], ~segmentation)
oxy_image[np.isnan(oxy_image)] = 0.
oxy_image[np.isinf(oxy_image)] = 0.
oxy_mean = np.mean(oxy_image)
oxy_image[0, 0] = 0.0
oxy_image[0, 1] = 1.
plot_image(oxy_image[:, :], plt.gca())
df_image_results = pd.DataFrame(data=np.expand_dims([self.image_name,
oxy_mean * 100.,
time], 0),
columns=["image name",
"oxygenation mean [%]",
"time to estimate"])
results_file = os.path.join(sc.get_full_dir("SMALL_BOWEL_RESULT"),
"results.csv")
if os.path.isfile(results_file):
df_results = pd.read_csv(results_file, index_col=0)
df_results = pd.concat((df_results, df_image_results)).reset_index(
drop=True
)
else:
df_results = df_image_results
df_results.to_csv(results_file)
plt.savefig(self.output().path,
dpi=250, bbox_inches='tight')
plt.close("all")
def run(self):
print "... read data"
segmentation_file = os.path.join(
sc.get_full_dir("COLORCHECKER_DATA"), "seg.tiff")
segmentation_file2 = os.path.join(
sc.get_full_dir("COLORCHECKER_DATA"), "seg2.tiff")
nrrd_reader = NrrdReader()
tiff_ring_reader = TiffRingReader()
# read the flatfield
flat = nrrd_reader.read(self.input()[0].path)
dark = nrrd_reader.read(self.input()[2].path)
# read the msi
nr_filters = len(sc.other["RECORDED_WAVELENGTHS"])
msi, segmentation = tiff_ring_reader.read(self.input()[1].path,
nr_filters,
segmentation=segmentation_file)
msi_copy = copy.deepcopy(msi) # copy to be able to apply both
# segmentations
msimani.apply_segmentation(msi, segmentation)
msi2, segmentation2 = tiff_ring_reader.read(self.input()[1].path,
nr_filters,
segmentation=segmentation_file2)
msimani.apply_segmentation(msi2, segmentation2)
msimani.apply_segmentation(msi_copy, segmentation + segmentation2)
# read the spectrometer measurement
msi_spectrometer = nrrd_reader.read(self.input()[3].path)
# correct by flatfield and dark image
#msimani.image_correction(msi, flat, dark)
#msimani.image_correction(msi2, flat, dark)
#msimani.image_correction(msi_copy, flat, dark)
msimani.dark_correction(msi, dark)
msimani.dark_correction(msi2, dark)
msimani.dark_correction(msi_copy, dark)
# create artificial rgb
rgb_image = msi_copy.get_image()[:, :, [2, 3, 1]]
rgb_image /= np.max(rgb_image)
rgb_image *= 255.
# preprocess the image
# sortout unwanted bands
print "... apply normalizations"
# normalize to get rid of lighting intensity
norm.standard_normalizer.normalize(msi)
norm.standard_normalizer.normalize(msi2)
print "... plot"
# plot of the rgb image
rgb_image = rgb_image.astype(np.uint8)
im = Image.fromarray(rgb_image, 'RGB')
enh_brightness = ImageEnhance.Brightness(im)
im = enh_brightness.enhance(2.)
plotted_image = np.array(im)
plt.figure()
f, (ax_rgb, ax_spectra) = plt.subplots(1, 2)
plot_image(plotted_image, ax_rgb, title="false rgb")
msiplot.plotMeanError(msi, ax_spectra)
msiplot.plotMeanError(msi2, ax_spectra)
standard_normalizer.normalize(msi_spectrometer)
msiplot.plot(msi_spectrometer, ax_spectra)
mean_spectrometer = msi_spectrometer.get_image()
mean_msi = msimani.calculate_mean_spectrum(msi).get_image()
mean_msi2 = msimani.calculate_mean_spectrum(msi2).get_image()
r2_msi = r2_score(mean_spectrometer, mean_msi)
r2_msi2 = r2_score(mean_spectrometer, mean_msi2)
ax_spectra.legend(["spectrocam 1 r2: " + str(r2_msi),
"spectrocam 2 r2: " + str(r2_msi2), "spectrometer"],
bbox_to_anchor=(0., 1.02, 1., .102), loc=3,
ncol=2, mode="expand", borderaxespad=0.,
fontsize=5)
plt.savefig(self.output().path,
dpi=250, bbox_inches='tight')
def run(self):
print "... read data"
segmentation_file = os.path.join(
sc.get_full_dir("COLORCHECKER_DATA"), "seg.tiff")
segmentation_file2 = os.path.join(
sc.get_full_dir("COLORCHECKER_DATA"), "seg2.tiff")
nrrd_reader = NrrdReader()
tiff_ring_reader = TiffRingReader()
# read the flatfield
flat = nrrd_reader.read(self.input()[0].path)
dark = nrrd_reader.read(self.input()[2].path)
# read the msi
nr_filters = len(sc.other["RECORDED_WAVELENGTHS"])
msi, segmentation = tiff_ring_reader.read(self.input()[1].path,
nr_filters,
segmentation=segmentation_file)
msi_copy = copy.deepcopy(msi) # copy to be able to apply both
# segmentations
msimani.apply_segmentation(msi, segmentation)
msi2, segmentation2 = tiff_ring_reader.read(self.input()[1].path,
nr_filters,
segmentation=segmentation_file2)
msimani.apply_segmentation(msi2, segmentation2)
msimani.apply_segmentation(msi_copy, segmentation + segmentation2)
# read the spectrometer measurement
msi_spectrometer = nrrd_reader.read(self.input()[3].path)
# correct by flatfield and dark image
#msimani.image_correction(msi, flat, dark)
#msimani.image_correction(msi2, flat, dark)
#msimani.image_correction(msi_copy, flat, dark)
msimani.dark_correction(msi, dark)
msimani.dark_correction(msi2, dark)
msimani.dark_correction(msi_copy, dark)
# create artificial rgb
rgb_image = msi_copy.get_image()[:, :, [2, 3, 1]]
rgb_image /= np.max(rgb_image)
rgb_image *= 255.
# preprocess the image
# sortout unwanted bands
print "... apply normalizations"
# normalize to get rid of lighting intensity
norm.standard_normalizer.normalize(msi)
norm.standard_normalizer.normalize(msi2)
print "... plot"
# plot of the rgb image
rgb_image = rgb_image.astype(np.uint8)
im = Image.fromarray(rgb_image, 'RGB')
enh_brightness = ImageEnhance.Brightness(im)
im = enh_brightness.enhance(2.)
plotted_image = np.array(im)
plt.figure()
f, (ax_rgb, ax_spectra) = plt.subplots(1, 2)
plot_image(plotted_image, ax_rgb, title="false rgb")
msiplot.plotMeanError(msi, ax_spectra)
msiplot.plotMeanError(msi2, ax_spectra)
standard_normalizer.normalize(msi_spectrometer)
msiplot.plot(msi_spectrometer, ax_spectra)
mean_spectrometer = msi_spectrometer.get_image()
mean_msi = msimani.calculate_mean_spectrum(msi).get_image()
mean_msi2 = msimani.calculate_mean_spectrum(msi2).get_image()
r2_msi = r2_score(mean_spectrometer, mean_msi)
r2_msi2 = r2_score(mean_spectrometer, mean_msi2)
ax_spectra.legend(["spectrocam 1 r2: " + str(r2_msi),
"spectrocam 2 r2: " + str(r2_msi2), "spectrometer"],
bbox_to_anchor=(0., 1.02, 1., .102), loc=3,
ncol=2, mode="expand", borderaxespad=0.,
fontsize=5)
plt.savefig(self.output().path,
dpi=250, bbox_inches='tight')
def run(self):
nrrd_reader = NrrdReader()
tiff_ring_reader = TiffRingReader()
# read the flatfield
flat = nrrd_reader.read(self.input()[1].path)
dark = nrrd_reader.read(self.input()[3].path)
# read the msi
nr_filters = len(sc.other["RECORDED_WAVELENGTHS"])
msi, segmentation = tiff_ring_reader.read(self.input()[2].path,
nr_filters)
# only take into account not saturated pixels.
segmentation = np.logical_and(
segmentation, (np.max(msi.get_image(), axis=-1) < 1000.))
# read the regressor
e_file = open(self.input()[0].path, 'r')
e = pickle.load(e_file)
# correct image setup
filter_nr = int(self.image_name[-6:-5])
original_order = np.arange(nr_filters)
new_image_order = np.concatenate(
(original_order[nr_filters - filter_nr:],
original_order[:nr_filters - filter_nr]))
# resort msi to restore original order
msimani.get_bands(msi, new_image_order)
# correct by flatfield
msimani.image_correction(msi, flat, dark)
# create artificial rgb
rgb_image = msi.get_image()[:, :, [2, 3, 1]]
rgb_image /= np.max(rgb_image)
rgb_image *= 255.
# preprocess the image
# sortout unwanted bands
print "1"
# zero values would lead to infinity logarithm, thus clip.
msi.set_image(np.clip(msi.get_image(), 0.00001, 2.**64))
# normalize to get rid of lighting intensity
norm.standard_normalizer.normalize(msi)
# transform to absorption
msi.set_image(-np.log(msi.get_image()))
# normalize by l2 for stability
norm.standard_normalizer.normalize(msi, "l2")
print "2"
# estimate
sitk_image, time = estimate_image(msi, e)
image = sitk.GetArrayFromImage(sitk_image)
plt.figure()
print "3"
rgb_image = rgb_image.astype(np.uint8)
im = Image.fromarray(rgb_image, 'RGB')
enh_brightness = ImageEnhance.Brightness(im)
im = enh_brightness.enhance(10.)
plotted_image = np.array(im)
top_left_axis = plt.gca()
top_left_axis.imshow(plotted_image, interpolation='nearest')
top_left_axis.xaxis.set_visible(False)
top_left_axis.yaxis.set_visible(False)
plt.set_cmap("jet")
print "4"
# plot parametric maps
segmentation[0, 0] = 1
segmentation[0, 1] = 1
oxy_image = np.ma.masked_array(image[:, :, 0], ~segmentation)
oxy_image[np.isnan(oxy_image)] = 0.
oxy_image[np.isinf(oxy_image)] = 0.
oxy_mean = np.mean(oxy_image)
oxy_image[0, 0] = 0.0
oxy_image[0, 1] = 1.
plot_image(oxy_image[:, :], plt.gca())
df_image_results = pd.DataFrame(
data=np.expand_dims([self.image_name, oxy_mean * 100., time], 0),
columns=["image name", "oxygenation mean [%]", "time to estimate"])
results_file = os.path.join(sc.get_full_dir("SMALL_BOWEL_RESULT"),
"results.csv")
if os.path.isfile(results_file):
df_results = pd.read_csv(results_file, index_col=0)
df_results = pd.concat(
(df_results, df_image_results)).reset_index(drop=True)
else:
df_results = df_image_results
df_results.to_csv(results_file)
plt.savefig(self.output().path, dpi=250, bbox_inches='tight')
plt.close("all")