Merge branch 'props' into 'master'

Props

See merge request !2

.gitignore

@@ -5,4 +5,6 @@ __pycache__/
 fslgui.egg-info/
 run.sh
 /mockups
+/build
+/dist
 .vscode/

fsl/gui/core.py

+"""
+core functions for setting up and controlling GUIs
+
+"""
+import os
+import sys
+import json
+
+import wx
+import yaml
+import fsleyes_props as props
+
+import fsl.gui.exceptions as fslerrs
+import fsl.gui.views as fslviews
+import fsl.gui.widgets as fslwidgets
+
+allowedContainerWidgets = (
+    'column', 'row', 'group',
+    'page', 'notebook'
+    )
+
+allowedWidgets = (
+    *allowedContainerWidgets, 
+    'filepath', 'checkbox', 'choice',
+    'number', 'button', 'FsleyesImage'
+)
+
+allowedConfigKeys = (
+    'appName', 'windowSize', 'width',
+    'height', 'layout',
+    )
+
+allowedKeys = (
+    *allowedConfigKeys,
+    *allowedWidgets,
+    )
+
+
+def isGroupKey(key):
+    """
+    returns True is key == "group"
+
+    returns False otherwise
+    """
+    if key == "group":
+        return True
+    else:
+        return False
+
+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.
+
+    returns False otherwise
+
+    a container widget is not really intereactive for the user.
+    it holds other widgets as children
+    """
+    if key in allowedContainerWidgets:
+        return True
+    else:
+        return False
+
+def loadSpec(specFile):
+    """
+    return the loaded yaml data as a dict
+    """
+    with open(specFile) as sf:
+        spec = yaml.load(sf, Loader=yaml.FullLoader)
+    return spec
+
+def checkSpec(buildSpec):
+    """
+    make sure the build spec contains only expected fields
+    """
+    def dictCheck(d):
+        if type(d) is list:
+            for entry in d:
+                print(entry)
+                for k, v in entry.items():
+                    k, _ = parseWidgetKey(k)
+                    if k not in allowedKeys:
+                        raise fslerrs.NotAValidKey("{} is not an allowed buildSpec key".format(k))
+                    if type(v) is dict:
+                        dictCheck(v)
+    dictCheck(buildSpec)
+
+
+def layoutFrom(widget):
+    """
+    redo layout of all widgets up the parent tree from this widget.
+    Stop when we get to a frame. This was taken from a wx wiki post
+    """
+    while widget.GetParent():
+        widget.Layout()
+        widget = widget.GetParent()
+        widget.Layout()
+        if widget.IsTopLevel():
+            break
+
+def parseWidgetKey(key):
+    """
+    returns string tuple (key, tag)
+
+    the string "key" must not contain more than one underscore
+    """
+    parts = key.split(sep="_")
+    t = ""
+    if len(parts) == 1:
+        n = parts[0]
+    elif len(parts) == 2:
+        n = parts[0]
+        t = parts[-1]
+    elif len(parts) > 2:
+        raise Exception("keys must be in the forms 'key' or 'key_name'")
+    else:
+        n = ""
+    return n, t
+
+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
+
+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):
+    """
+    returns the appropriate widget creation function,
+    but does not return the actual widget instance.
+    That comes later.
+    """
+    widget = getattr(fslwidgets, key)
+    return widget
+
+def makeWidget(parent, propObj, key, tag, value):
+    """
+    returns the appropriate widget from a key string
+
+    key:    str parsed from the form "key_tag" or "key"
+    tag:    str parsed from the form "key_tag" 
+    value:  the dict value for this key. Only value==dict is used here
+
+    """
+    if key in allowedWidgets:
+        wid = widgetFromKey(key)
+        print('making widget: ', key)
+        if isinstance(value, dict):
+            w = wid(parent, propObj, **value)
+        else:
+            if isGroupKey(key):
+                w = wid(parent, tag)
+            else:
+                if isGroup(parent):
+                    w = addWidgetToGroup(parent, wid)
+                elif isNotebook(parent):
+                    w = wid(parent)
+                    w = addPageToNotebook(parent, w, tag)
+                else:
+                    w = wid(parent)
+    return w
+
+def layout(parent, buildSpec, propObj):
+    """
+    layout all allowed widgets in a buildSpec
+    """
+    for entry in buildSpec:
+        for k, v in entry.items():
+            k, t = parseWidgetKey(k)
+            w = makeWidget(parent, propObj, k, t, v,)
+            if not isPage(w):
+                parent.GetSizer().Add(w, proportion=0, flag=wx.ALL | wx.EXPAND, border=5)
+            layoutFrom(w)
+            if isContainerKey(k):
+                if type(v) is list:
+                    layout(w, v, propObj)
+    parent.Layout()
+    return parent
+
+
+def buildGUI(buildSpec, propObj):
+    """
+    build a GUI from a build spec dictionary (or JSON)
+    """
+    checkSpec(buildSpec)
+    mainWin = wx.Frame(None)
+
+    mainWin.SetTitle(buildSpec['appName'])
+    mainWin.SetSize((buildSpec['windowSize']['width'], buildSpec['windowSize']['height']))
+
+    mainSizer = wx.BoxSizer(wx.VERTICAL)
+    mainWin.SetSizer(mainSizer)
+    mainWin = layout(mainWin, buildSpec['layout'], propObj)
+
+    mainWin.Centre()
+    mainWin.Show()
+    return mainWin
+
+
+
+
+
+

fsl/gui/exceptions.py

+"""
+custom exceptions to be used in fslgui
+
+"""
+class NotAValidKey(Exception):
+    pass
+
+class MissingRequiredKey(Exception):
+    pass
+
+

fsl/gui/guis.py

@@ -9,6 +9,9 @@ import random
 
 import wx
 from fsl.data import image
+import fsleyes_props as props
+#from fsleyes_props.build import buildGUI
+props.initGUI()
 
 import fsl.gui.views as fslviews
 import fsl.gui.tools as fsltools
@@ -210,4 +213,7 @@ class FlirtGui(BaseGui):
         else:
             self.view.input.set_label("Input image*")
             self.view.input_lowres.Hide()
-            self._layout_from(self.view.input_lowres)
\ No newline at end of file
+            self._layout_from(self.view.input_lowres)
+
+
+

fsl/gui/scripts/bet_gui.py

 #!/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

+#!/usr/bin/env python
+
+import sys
+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
+
+def run(p, button):
+    print('RUN COMMAND: ')
+    print(p.command())
+
+class Pnm(props.HasProperties):
+    """
+    Pnm is the data model for PnmGui
+    """
+
+    physioFile = props.FilePath(required=True, exists=True)
+    imageFile = props.FilePath(required=True, exists=True)
+
+    sliceOrderChoices = OrderedDict((
+        ('up', 'Up'),
+        ('down', 'Down'),
+        ('iup', 'Interleaved Up'),
+        ('idown', 'Interleaved Down'),
+        ('file', 'User Specified File')
+        ))
+
+    scannerSliceDirChoices = OrderedDict((
+        ('x', 'X'),
+        ('y', 'Y'),
+        ('z', 'Z')
+        ))
+
+    idxCardiac = props.Int(minval=0, slider=False)
+    idxResp = props.Int(minval=0, slider=False)
+    idxTrig = props.Int(minval=0, slider=False)
+
+    pulseOxTrig = props.Boolean()
+
+    sampleRate = props.Int(minVal=0, slider=False)
+    tr = props.Real(precision=0.01, slider=False)
+
+    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)
+
+    orderCardiacEV = props.Int(minVal=0, slider=False)
+    orderRespEV = props.Int(minVal=0, slider=False)
+    orderCardiacIntEV = props.Int(minVal=0, slider=False)
+    orderRespIntEV = props.Int(minVal=0, slider=False)
+
+    rvt = props.Boolean()
+    heartRate = props.Boolean()
+    csf = props.Boolean()
+
+    csfFile = props.FilePath(required=False, exists=True)
+
+    cardiacSmoothSec = props.Real(precision=0.001, slider=False)
+    respSmoothSec = props.Real(precision=0.001, slider=False)
+    hrSmoothSec = props.Real(precision=0.001, slider=False)
+    rvtSmoothSec = props.Real(precision=0.001, slider=False)
+
+    applyCleanup = props.Boolean()
+    invertRespTrace = props.Boolean()
+    invertCardiacTrace = props.Boolean()
+
+    runButton = props.Button(text='Run', callback=run)
+
+    def command(self):
+        return "pnm_stage1 blah blah blah"
+
+
+    def __init__(
+            self,
+            **kwargs
+            ):
+        super().__init__(**kwargs)
+
+def main():
+    # get an app instance
+    app = wx.App()
+    pnm = Pnm()
+    pnmView = core.loadSpec(fslViews.pnm)
+    gui = core.buildGUI(pnmView, pnm)
+    app.MainLoop()
+if __name__ == "__main__":
+    sys.exit(main())

fsl/gui/tools.py

@@ -8,9 +8,11 @@ tools are models that store data and allow FSL tools to be called from other pyt
 # Author: Taylor Hanayik <hanayik@gmail.com>
 import os
 import subprocess
+from collections import OrderedDict
 
-from fsl.utils import idle
 
+from fsl.utils import idle
+import fsleyes_props as props
 
 
 class Bet(object):
@@ -318,3 +320,5 @@ class Flirt(object):
                 search_zmax=90
                 ):
         pass
+
+

fsl/gui/view_specs/bet_spec.yaml

+---
+# the pnm view layout specification
+appName: BET
+windowSize:
+  width: 800
+  height: 500
+layout:
+  - notebook:
+    - page_Inputs:
+      - group_Files:
+        - column:
+          - filepath: {label: Input file, propName: inputFile}
+          - filepath: {label: Output file, propName: outputFile}
+      - row:
+        - number: {label: F value, propName: fval, showLimits: 0}
+      - column:
+        - FsleyesImage: {name: FsleyesImage}
+    - page_Options:
+      - column:
+        - choice: {label: BET run type, propName: betRunType}
\ No newline at end of file

fsl/gui/view_specs/pnm_spec.yaml

+---
+# the pnm view layout specification
+appName: PNM
+windowSize:
+  width: 800
+  height: 840
+layout:
+  - 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

 #!/usr/bin/env python
-#
-# bet_view.py
-#
-# Author: Taylor Hanayik <hanayik@gmail.com>
+"""
+views are the graphical layouts of windows.
+
+User interaction is controlled by guis.py.
+
+Data is stored and updated using tools.py
+
+Author: Taylor Hanayik, hanayik@gmail.com
+
+"""
+
+
+from os.path import dirname, join, abspath
 
 import wx
 import wx.lib.scrolledpanel as scrolled
@@ -201,7 +210,7 @@ class BetView(wx.Panel):
         self.SetSizer(sizer)
 
 
-class PnmView(wx.Panel):
+class NotUsedPnmView(wx.Panel):
     """
     PnmView defines the graphical layout of widgets for the PNM gui
     """
@@ -209,6 +218,15 @@ class PnmView(wx.Panel):
         super().__init__(parent)
         sizer = wx.BoxSizer(wx.VERTICAL)
 
+        # init title panel
+        self.title_panel = fslwidgets.Title(self, title=title)
+        # add title panel
+        sizer.Add(self.title_panel, proportion=0, flag=wx.ALIGN_CENTER | wx.ALL, border=5)
+
+        #
+        # lastly set the sizer with all widgets added 
+        self.SetSizer(sizer)
+
 
 class FlirtView(wx.Panel):
     """
@@ -240,7 +258,7 @@ class FlirtView(wx.Panel):
         self.input_lowres = fslwidgets.Input(self).set_label("Low res image*")
         sizer.Add(self.input_lowres, proportion=0, flag=wx.EXPAND | wx.ALL, border=5)
         self.input_lowres.Hide()
-        
+
         # high res input panel
         self.input = fslwidgets.Input(self).set_label("Input image*")
         sizer.Add(self.input, proportion=0, flag=wx.EXPAND | wx.ALL, border=5)
@@ -259,12 +277,18 @@ class FlirtView(wx.Panel):
         # lastly set the sizer with all widgets added 
         self.SetSizer(sizer)
 
-    
+
+
+VIEW_PATH = join(abspath(dirname(__file__)), 'view_specs')
+pnm = join(VIEW_PATH, 'pnm_spec.yaml')
+bet = join(VIEW_PATH, 'bet_spec.yaml')
+
+
+
 
 class FslView():
     """
     FslView is the main FSL start window. not to be 
     confused with the deprecated image viewer fslview (RIP)
     """
-    
 

fsl/gui/widgets.py

@@ -13,12 +13,120 @@ import fsleyes.views.orthopanel as orthopanel
 import fsleyes.profiles as profiles
 import fsleyes.profiles.profilemap as profilemap
 import fsleyes.colourmaps as colourmaps
+import fsleyes_props as props
 
 from fsl.utils.platform import platform as fslplatform
 from fsl.utils import idle
-
 import fsl.data.image as fslimage
+
 import fsl.gui.icons as fslicons