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Commit 4e53b71a authored by Taylor Hanayik's avatar Taylor Hanayik
Browse files

add notebooks and pages

parent 847dc781
Hide whitespace changes
Inline Side-by-side
fsl/gui/core.py
View file @ 4e53b71a
......@@ -16,6 +16,7 @@ import fsl.gui.widgets as fslwidgets
allowedContainerWidgets = (
'column', 'row', 'group',
'page', 'notebook'
)
allowedWidgets = (
......@@ -35,7 +36,7 @@ allowedKeys = (
)
def isGroup(key):
def isGroupKey(key):
"""
returns True is key == "group"
......@@ -46,7 +47,18 @@ def isGroup(key):
else:
return False
def isContainer(key):
def isPageKey(key):
"""
returns True is key == "group"
returns False otherwise
"""
if key == "page":
return True
else:
return False
def isContainerKey(key):
"""
returns True if this key is associated with a container widget
from allowedContainerWidgets.
......@@ -117,8 +129,20 @@ def parseWidgetKey(key):
n = ""
return n, t
def parentIsGroup(parent):
if isinstance(parent.GetSizer(), wx.StaticBoxSizer):
def isGroup(widget):
if isinstance(widget.GetSizer(), wx.StaticBoxSizer):
return True
else:
return False
def isNotebook(widget):
if isinstance(widget, wx.Notebook):
return True
else:
return False
def isPage(widget):
if isinstance(widget.GetParent(), wx.Notebook):
return True
else:
return False
......@@ -127,6 +151,10 @@ def addWidgetToGroup(parent, widget):
w = widget(parent.GetSizer().GetStaticBox())
return w
def addPageToNotebook(parent, widget, name):
parent.AddPage(widget, name)
return widget
def widgetFromKey(key):
"""
......@@ -148,14 +176,18 @@ def makeWidget(parent, propObj, key, tag, value):
"""
if key in allowedWidgets:
wid = widgetFromKey(key)
print('making widget: ', key)
if isinstance(value, dict):
w = wid(parent, propObj, **value)
else:
if isGroup(key):
if isGroupKey(key):
w = wid(parent, tag)
else:
if parentIsGroup(parent):
if isGroup(parent):
w = addWidgetToGroup(parent, wid)
elif isNotebook(parent):
w = wid(parent)
w = addPageToNotebook(parent, w, tag)
else:
w = wid(parent)
return w
......@@ -168,9 +200,10 @@ def layout(parent, buildSpec, propObj):
for k, v in entry.items():
k, t = parseWidgetKey(k)
w = makeWidget(parent, propObj, k, t, v,)
parent.GetSizer().Add(w, proportion=0, flag=wx.ALL | wx.EXPAND, border=5)
if not isPage(w):
parent.GetSizer().Add(w, proportion=0, flag=wx.ALL | wx.EXPAND, border=5)
layoutFrom(w)
if isContainer(k):
if isContainerKey(k):
if type(v) is list:
layout(w, v, propObj)
parent.Layout()
......
fsl/gui/scripts/bet_gui.py
View file @ 4e53b71a
#!/usr/bin/env python
import wx
import sys
from fsl.gui.guis import BetGui
import argparse
from collections import OrderedDict
import wx
import yaml
from fsl.utils import idle
import fsleyes_props as props
import fsl.gui.core as core
import fsl.gui.views as fslViews
import fsl.gui.tools as fslTools
class Bet(props.HasProperties):
"""
Bet is the data model for Bet Gui
"""
betRunChoices = OrderedDict((
('default', 'Default Brain extraction'),
('robust', 'Robust'),
('eyeClean', 'Eye and optic nerve cleanup'),
('biasAndNeckClean', 'Bias field and neck Clean'),
('smallZ', 'Brain has small Z FOV'),
('4d', 'Apply to 4D fMRI'),
('withBetSurf', 'Also run betsurf'),
('withBetSurfT2', 'Run betsurf with additional T2 image')
))
inputFile = props.FilePath(required=True, exists=True)
outputFile = props.FilePath(required=True, exists=False)
fval = props.Real(precision=0.001, minval=0, maxval=1, clamped=True)
betRunType = props.Choice(choices=list(betRunChoices.values()))
parser = argparse.ArgumentParser(description="FSL's brain extraction tool")
def __init__(
self,
**kwargs
):
super().__init__(**kwargs)
def main():
args = parser.parse_args()
# get an app instance
app = wx.App()
frame = wx.Frame(None, size=(800, 600))
sizer = wx.BoxSizer(wx.VERTICAL)
betgui = BetGui(frame, "BET")
sizer.Add(betgui.view, proportion=1, flag=wx.EXPAND | wx.ALL, border=5)
frame.SetSizer(sizer)
frame.Centre()
frame.Show()
bet = Bet()
betView = core.loadSpec(fslViews.bet)
gui = core.buildGUI(betView, bet)
app.MainLoop()
if __name__ == "__main__":
sys.exit(main())
fsl/gui/scripts/pnm_gui.py
View file @ 4e53b71a
......@@ -48,8 +48,8 @@ class Pnm(props.HasProperties):
sampleRate = props.Int(minVal=0, slider=False)
tr = props.Real(precision=0.01, slider=False)
sliceOrder = props.Choice(choices=list(sliceOrderChoices.keys()))
sliceDir = props.Choice(choices=list(scannerSliceDirChoices.keys()))
sliceOrder = props.Choice(choices=list(sliceOrderChoices.values()))
sliceDir = props.Choice(choices=list(scannerSliceDirChoices.values()))
sliceTimeFile = props.FilePath(required=False, exists=True)
outputFile = props.FilePath(required=True, exists=False)
......
fsl/gui/view_specs/bet_spec.yaml 0 → 100644
View file @ 4e53b71a
---
# the pnm view layout specification
appName: BET
windowSize:
width: 800
height: 500
layout:
- notebook:
- page_Setup:
- group_Files:
- column:
- filepath: {label: Input file, propName: inputFile}
- filepath: {label: Output file, propName: outputFile}
- row:
- number: {label: F value, propName: fval, showLimits: 0}
- page_Options:
- column:
- choice: {label: BET run type, propName: betRunType}
- page_Viewer:
\ No newline at end of file
fsl/gui/view_specs/pnm_spec.yaml
View file @ 4e53b71a
......@@ -5,47 +5,50 @@ windowSize:
width: 800
height: 840
layout:
- group_Input:
- column:
- filepath: {label: Physio file, propName: physioFile}
- filepath: {label: Image file, propName: imageFile}
- group_Format:
- row:
- number: {label: Caridac column, propName: idxCardiac}
- number: {label: Respitory column, propName: idxResp}
- number: {label: Scan Trig column, propName: idxTrig}
- row:
- checkbox: {label: Pulse Ox Trig, propName: pulseOxTrig}
- number: {label: Sample Rate (Hz), propName: sampleRate}
- number: {label: TR (sec), propName: tr}
- row:
- choice: {label: Slice Order, propName: sliceOrder}
- filepath: {label: Slice time file, propName: sliceTimeFile}
- choice: {label: Slice Direction, propName: sliceDir}
- group_Output:
- column:
- filepath: {label: Output file, propName: outputFile}
- group_EVs:
- row:
- number: {label: Cardiac EV order, propName: orderCardiacEV}
- number: {label: Resp EV order, propName: orderRespEV}
- number: {label: Cariac interaction EV order, propName: orderCardiacIntEV}
- number: {label: Resp interaction EV order, propName: orderRespIntEV}
- row:
- checkbox: {label: RVT, propName: rvt}
- checkbox: {label: Heart Rate, propName: heartRate}
- checkbox: {label: CSF, propName: csf}
- column:
- filepath: {label: CSF mask, propName: csfFile}
- group_Advanced:
- row:
- number: {label: Cardiac smooth (sec), propName: cardiacSmoothSec}
- number: {label: Resp smooth (sec), propName: respSmoothSec}
- number: {label: HR smooth (sec), propName: hrSmoothSec}
- number: {label: RVT smooth (sec), propName: rvtSmoothSec}
- row:
- checkbox: {label: Clean up, propName: applyCleanup}
- checkbox: {label: Invert resp trace, propName: invertRespTrace}
- checkbox: {label: Invert cardiac trace, propName: invertCardiacTrace}
- notebook:
- page_Setup:
- group_Input:
- column:
- filepath: {label: Physio file, propName: physioFile}
- filepath: {label: Image file, propName: imageFile}
- group_Format:
- row:
- number: {label: Caridac column, propName: idxCardiac}
- number: {label: Respitory column, propName: idxResp}
- number: {label: Scan Trig column, propName: idxTrig}
- row:
- checkbox: {label: Pulse Ox Trig, propName: pulseOxTrig}
- number: {label: Sample Rate (Hz), propName: sampleRate}
- number: {label: TR (sec), propName: tr}
- row:
- choice: {label: Slice Order, propName: sliceOrder}
- filepath: {label: Slice time file, propName: sliceTimeFile}
- choice: {label: Slice Direction, propName: sliceDir}
- group_Output:
- column:
- filepath: {label: Output file, propName: outputFile}
- group_EVs:
- row:
- number: {label: Cardiac EV order, propName: orderCardiacEV}
- number: {label: Resp EV order, propName: orderRespEV}
- number: {label: Cariac interaction EV order, propName: orderCardiacIntEV}
- number: {label: Resp interaction EV order, propName: orderRespIntEV}
- row:
- checkbox: {label: RVT, propName: rvt}
- checkbox: {label: Heart Rate, propName: heartRate}
- checkbox: {label: CSF, propName: csf}
- column:
- filepath: {label: CSF mask, propName: csfFile}
- page_Advanced:
- row:
- number: {label: Cardiac smooth (sec), propName: cardiacSmoothSec}
- number: {label: Resp smooth (sec), propName: respSmoothSec}
- number: {label: HR smooth (sec), propName: hrSmoothSec}
- number: {label: RVT smooth (sec), propName: rvtSmoothSec}
- row:
- checkbox: {label: Clean up, propName: applyCleanup}
- checkbox: {label: Invert resp trace, propName: invertRespTrace}
- checkbox: {label: Invert cardiac trace, propName: invertCardiacTrace}
- page_Plots:
- row:
- button: {label: Run, propName: runButton}
\ No newline at end of file
fsl/gui/views.py
View file @ 4e53b71a
......@@ -281,6 +281,7 @@ class FlirtView(wx.Panel):
VIEW_PATH = join(abspath(dirname(__file__)), 'view_specs')
pnm = join(VIEW_PATH, 'pnm_spec.yaml')
bet = join(VIEW_PATH, 'bet_spec.yaml')
......
fsl/gui/widgets.py
View file @ 4e53b71a
......@@ -64,6 +64,23 @@ def group(parent, label):
panel.SetSizer(bsizer)
return panel
def notebook(parent):
"""
noetbook
"""
notebook = wx.Notebook(parent)
return notebook
def page(parent):
"""
page
"""
panel = wx.Panel(parent)
sizer = wx.BoxSizer(wx.VERTICAL)
panel.SetSizer(sizer)
panel.SetBackgroundColour(wx.NullColour)
return panel
def filepath(parent, propobj, **kwargs):
if kwargs.get('label') == None:
raise fslerrs.MissingRequiredKey("A 'label' key must be provided to a FilePath")
......@@ -92,9 +109,9 @@ def number(parent, propobj, **kwargs):
raise fslerrs.MissingRequiredKey("A 'label' key must be provided to a Checkbox")
panel = wx.Panel(parent)
panel.SetSizer(wx.BoxSizer(wx.HORIZONTAL))
st = wx.StaticText(panel, label=kwargs['label'])
st = wx.StaticText(panel, label=kwargs.pop('label'))
panel.GetSizer().Add(st, proportion=0, flag=wx.ALL | wx.ALIGN_CENTER_VERTICAL, border=2)
prp = props.widgets.makeWidget(panel, propobj, kwargs['propName'])
prp = props.widgets.makeWidget(panel, propobj, **kwargs)
panel.GetSizer().Add(prp, proportion=0, flag=wx.ALL | wx.EXPAND, border=5)
return panel
......
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