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Improvements to reporting of output perfusion data
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@mcraig-ibme
mcraig-ibme committed Dec 12, 2018
1 parent 180687b commit c702460
Showing 1 changed file with 63 additions and 40 deletions.
103 changes: 63 additions & 40 deletions oxasl/oxford_asl.py
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Original file line number Diff line number Diff line change
Expand Up @@ -278,8 +278,8 @@ def model_paired(wsp):

# Generate PVM and PWM maps for Basil
struc.segment(wsp)
wsp.structural.wm_pv_asl = reg.struc2asl(wsp, wsp.structural.wm_pv, use_applywarp=True)
wsp.structural.gm_pv_asl = reg.struc2asl(wsp, wsp.structural.gm_pv, use_applywarp=True)
wsp.structural.wm_pv_asl = reg.struc2asl(wsp, wsp.structural.wm_pv)
wsp.structural.gm_pv_asl = reg.struc2asl(wsp, wsp.structural.gm_pv)
wsp.basil_options = {"pwm" : wsp.structural.wm_pv_asl, "pgm" : wsp.structural.gm_pv_asl}
basil.basil(wsp, output_wsp=wsp.sub("basil_pvcorr"), prefit=False)
output_native(wsp.output, wsp.basil_pvcorr)
Expand Down Expand Up @@ -313,65 +313,88 @@ def do_report(wsp):
wsp.report.generate_html(report_dir, report_build_dir)
wsp.log.write(" - Report generated in %s\n" % report_dir)

def output_native(wsp, basil_wsp):
OUTPUT_ITEMS = {
"mean_ftiss" : ("perfusion", 6000, True, "ml/100g/min", "30-50", "10-20"),
"mean_fblood" : ("aCBV", 100, True, "ml/100g/min", "", ""),
"mean_delttiss" : ("arrival", 1, False, "s", "", ""),
"mean_fwm" : ("perfusion_wm", 6000, True, "ml/100g/min", "", "10-20"),
"mean_deltwm" : ("arrival_wm", 1, False, "s", "", ""),
"modelfit" : ("modelfit", 1, False, "", "", ""),
}

def output_native(wsp, basil_wsp, report=None):
"""
Create native space output images
:param wsp: Workspace object. Output will be placed in a sub workspace named ``native``
:param basil_wsp: Workspace in which Basil modelling has been run. The ``finalstep``
attribute is expected to point to the final output workspace
"""
output_items = {
"mean_ftiss" : ("perfusion", 6000, True, "ml/100g/min", "?"),
"mean_fblood" : ("aCBV", 100, True, "ml/100g/min", "?"),
"mean_delttiss" : ("arrival", 1, False, "s", "?"),
"mean_fwm" : ("perfusion_wm", 6000, True, "ml/100g/min", "?"),
"mean_deltwm" : ("arrival_wm", 1, False, "s", "?"),
"modelfit" : ("modelfit", 1, False, "", "?"),
}
wsp.sub("native")
for fabber_output, oxasl_output in output_items.items():
for fabber_output, oxasl_output in OUTPUT_ITEMS.items():
img = basil_wsp.finalstep.ifnone(fabber_output, None)
if img is not None:
# Make negative values = 0 and ensure masked value zeroed
data = np.copy(img.data)
data[img.data < 0] = 0
data[wsp.rois.mask.data == 0] = 0
img = Image(data, header=img.header)
name, multiplier, is_perfusion, units, norm_range = oxasl_output
if is_perfusion:
name, multiplier, calibrate, _, _, _ = oxasl_output
if calibrate:
img, = corrections.apply_sensitivity_correction(wsp, img)
setattr(wsp.native, name, img)
if is_perfusion and wsp.calib is not None:
if calibrate and wsp.calib is not None:
alpha = wsp.ifnone("alpha", 0.85 if wsp.asldata.casl else 0.98)
img = calib.calibrate(wsp, img, multiplier=multiplier, alpha=alpha)
name = "%s_calib" % name
setattr(wsp.native, name, img)

# Reporting
if img.ndim == 3:
page = wsp.report.page(name)
page.heading("Output image: %s" % name)
if name.endswith("_calib"):
page.heading("Calibration", level=1)
page.text("Image was calibrated using supplied M0 image")
page.text("Inversion efficiency: %f" % alpha)
page.text("Multiplier for physical units: %f" % multiplier)

page.heading("Metrics", level=1)
table = []
table.append(["Mean within mask", "%.4g %s" % (np.mean(img[wsp.rois.mask.data > 0.5]), units), norm_range])
if wsp.structural.struc is not None:
gm_asl = reg.struc2asl(wsp, wsp.structural.gm_pv)
wm_asl = reg.struc2asl(wsp, wsp.structural.wm_pv)
table.append(["GM mean", "%.4g %s" % (np.mean(img[gm_asl.data > 0.5]), units), norm_range])
table.append(["Pure GM mean", "%.4g %s" % (np.mean(img[gm_asl.data > 0.8]), units), norm_range])
table.append(["WM mean", "%.4g %s" % (np.mean(img[wm_asl.data > 0.5]), units), norm_range])
table.append(["Pure WM mean", "%.4g %s" % (np.mean(img[wm_asl.data > 0.9]), units), norm_range])
page.table(table, headers=["Metric", "Value", "Typical"])

page.heading("Image", level=1)
page.image("%s_img" % name, LightboxImage(img, zeromask=False, mask=wsp.rois.mask, colorbar=True))

output_report(wsp.native, report=report)

def output_report(wsp, report=None):
"""
Create report pages from output data
:param wsp: Workspace object containing output
"""
if report is None:
report = wsp.report

roi = wsp.rois.mask.data
if wsp.structural.struc is not None:
gm = reg.struc2asl(wsp, wsp.structural.gm_pv).data
wm = reg.struc2asl(wsp, wsp.structural.wm_pv).data

for oxasl_name, multiplier, calibrate, units, normal_gm, normal_wm in OUTPUT_ITEMS.values():
name = oxasl_name + "_calib"
img = getattr(wsp, name)
if img is None:
name = oxasl_name
img = getattr(wsp, name)

if img is not None and img.ndim == 3:
page = report.page(name)
page.heading("Output image: %s" % name)
if calibrate and name.endswith("_calib"):
alpha = wsp.ifnone("alpha", 0.85 if wsp.asldata.casl else 0.98)
page.heading("Calibration", level=1)
page.text("Image was calibrated using supplied M0 image")
page.text("Inversion efficiency: %f" % alpha)
page.text("Multiplier for physical units: %f" % multiplier)

page.heading("Metrics", level=1)
data = img.data
table = []
table.append(["Mean within mask", "%.4g %s" % (np.mean(data[roi > 0.5]), units), ""])
if wsp.structural.struc is not None:
table.append(["GM mean", "%.4g %s" % (np.mean(data[gm > 0.5]), units), normal_gm])
table.append(["Pure GM mean", "%.4g %s" % (np.mean(data[gm > 0.8]), units), normal_gm])
table.append(["WM mean", "%.4g %s" % (np.mean(data[wm > 0.5]), units), normal_wm])
table.append(["Pure WM mean", "%.4g %s" % (np.mean(data[wm > 0.9]), units), normal_wm])
page.table(table, headers=["Metric", "Value", "Typical"])

page.heading("Image", level=1)
page.image("%s_img" % name, LightboxImage(img, zeromask=False, mask=wsp.rois.mask, colorbar=True))

def output_trans(wsp):
"""
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