ViPEr, a Visual programming Environment for Python · Michel F. SANNER TSRI 2002 ViPEr, a Visual...

Michel F. SANNER TSRI 2002

ViPErViPEr, a Visual, a Visualprogramming Environmentprogramming Environment

for Pythonfor Python

Michel F. Sanner, Daniel Stoffler

The Scripps Research InstituteLa Jolla, California

The Molecular Graphics Laboratory

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CalTech Pasadena CA. Sept. 2002

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AcknowledgmentAcknowledgmento NIH - NBCR (Peter Arzberger)

? 5 NCRR representedo NBCR (SDSC)o NCMI (Baylor college)o Computer Graphics Lab (UCSF)o MMTSB (TSRI)o MMMB

o Camera men: Art Olson, Chenglong Lio Enthought: Eric Jones, Travis Vaughto Michael Aivasis, CalTech

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SCHEDULESCHEDULE

o I –AVSo II – ViPEr

? Basics, Architecture, Libraries

? Nodes, Execution Flow, Widgets, Data Types

o III - Demos

o IV - Conclusion

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AVS-5: AVS-5: Advanced Visualization System Inc.Advanced Visualization System Inc.

Enabling scientists (non-programmers)to build computational networksEnabling scientists (non-programmers)to build computational networks

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Lessons learn from AVS-5Lessons learn from AVS-5o GOOD:

? Modularity / extensibility / code-reuse? Enabling scientists (non-programmers) to

build computational networkso BAD:

? Application centric? Lack of programmability? Limited sets of data types? Hard to add new nodes

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Python to the rescuePython to the rescue

High level language as a scripting environmentHigh level language as a scripting environment

MolecularSurfaces

Molecular

MolecularSurfaces

Surfaces

Molecules

Molecules

Molecules

DataBase

DataDataBaseBaseElectrostatics

Electrostatics

Electrostatics

DelaunayDelaunayDelaunay

Homology

Homology

HomologyCSGCSGCSG

3DViewer

3D3DViewerViewer

MM-MDMM-MDMM-MD

NewMethod

NewNewMethodMethod

Your

MethodYourYour

MethodMethod

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ViPErViPEr: almost AVS-5: almost AVS-5

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ViPErViPEr: NOT AVS-5: NOT AVS-5

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Demo 1Demo 1

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Architecture OverviewArchitecture Overview

NetworEditor

ViPEr

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LibrariesLibraries

Standard 3D Viewer Misc.MolKitSymServerImageLibCCP4…

DejaVu

MolKitsymservPIL

ViPER Libraries Python Packages

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NetworkNodeNetworkNode

MyNode

Input PortName: inPort1Type: StringRequired: 1

Output Portname: outPort1Type: None

‘myfile.dat’ ‘file1.dat’

[myfile.dat’, ‘file1.dat’]

def doit(self, inPort1): out =[] for n in names: out.append( read(n)) self.outputData(outPort1=out)

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NetworkNodeNetworkNodeclass ReadImage(NetworkNode): """based on the Image.open function. Reads an image file Input: filename (string) Output: Image""" def __init__(self, name='Read Image'): NetworkNode.__init__(self, name=name) self.readOnly = 1 self.inputPortsDescr.append( {'name':'filename', 'datatype':‘string’} ) self.outputPortsDescr.append( {'name':'image', 'datatype':’image’ } )

self.widgetDescr['filename'] = {'class':NEEntryWithFileBrowser, 'master':'node', 'filetypes': [('all', '*')], 'title':'read image’, 'width':10 } code = """def doit(self, filename): import Image im = Image.open(filename) if im: self.outputData(image=im)\n""" self.setFunction(code)

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class ReadImage(NetworkNode): """based on the Image.open function. Reads an image file Input: filename (string) Output: Image""" def __init__(self, name='Read Image'): NetworkNode.__init__(self, name=name) self.readOnly = 1 self.inputPortsDescr.append( {'name':'filename', 'datatype':‘string’} ) self.outputPortsDescr.append( {'name':'image', 'datatype':’image’ } )

self.widgetDescr['filename'] = {'class':NEEntryWithFileBrowser, 'master':'node', 'filetypes': [('all', '*')], 'title':'read image’, 'width':10 } code = """def doit(self, filename): import Image im = Image.open(filename) if im: self.outputData(image=im)\n""" self.setFunction(code)

NetworkNodeNetworkNode

SubclassNetworkNode

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NetworkNodeNetworkNodeclass ReadImage(NetworkNode): """based on the Image.open function. Reads an image file Input: filename (string) Output: Image""" def __init__(self, name='Read Image'): NetworkNode.__init__(self, name=name) self.readOnly = 1 self.inputPortsDescr.append( {'name':'filename', 'datatype':‘string’} ) self.outputPortsDescr.append( {'name':'image', 'datatype':’image’ } )

self.widgetDescr['filename'] = {'class':NEEntryWithFileBrowser, 'master':'node', 'filetypes': [('all', '*')], 'title':'read image’, 'width':10 } code = """def doit(self, filename): import Image im = Image.open(filename) if im: self.outputData(image=im)\n""" self.setFunction(code)

Doc string:will serve as the tooltipin the nodes library

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NetworkNodeNetworkNodeclass ReadImage(NetworkNode): """based on the Image.open function. Reads an image file Input: filename (string) Output: Image""" def __init__(self, name='Read Image'): NetworkNode.__init__(self, name=name) self.readOnly = 1 self.inputPortsDescr.append( {'name':'filename', 'datatype':‘string’} ) self.outputPortsDescr.append( {'name':'image', 'datatype':’image’ } )

self.widgetDescr['filename'] = {'class':NEEntryWithFileBrowser, 'master':'node', 'filetypes': [('all', '*')], 'title':'read image’, 'width':10 } code = """def doit(self, filename): import Image im = Image.open(filename) if im: self.outputData(image=im)\n""" self.setFunction(code)

This node will N0Tbe editable by a user

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NetworkNodeNetworkNodeclass ReadImage(NetworkNode): """based on the Image.open function. Reads an image file Input: filename (string) Output: Image""" def __init__(self, name='Read Image'): NetworkNode.__init__(self, name=name) self.readOnly = 1 self.inputPortsDescr.append( {'name':'filename', 'datatype':‘string’} ) self.outputPortsDescr.append( {'name':'image', 'datatype':’image’ } )

self.widgetDescr['filename'] = {'class':NEEntryWithFileBrowser, 'master':'node', 'filetypes': [('all', '*')], 'title':'read image’, 'width':10 } code = """def doit(self, filename): import Image im = Image.open(filename) if im: self.outputData(image=im)\n""" self.setFunction(code)

Input ports description: required arguments: name: string optional arguments: required: (0,1) datatype: type ballons: string noWidgetValue: value

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NetworkNodeNetworkNodeclass ReadImage(NetworkNode): """based on the Image.open function. Reads an image file Input: filename (string) Output: Image""" def __init__(self, name='Read Image'): NetworkNode.__init__(self, name=name) self.readOnly = 1 self.inputPortsDescr.append( {'name':'filename', 'datatype':‘string’} ) self.outputPortsDescr.append( {'name':'image', 'datatype':’image’ } )

self.widgetDescr['filename'] = {'class':NEEntryWithFileBrowser, 'master':'node', 'filetypes': [('all', '*')], 'title':'read image’, 'width':10 } code = """def doit(self, filename): import Image im = Image.open(filename) if im: self.outputData(image=im)\n""" self.setFunction(code)

Output ports description: required arguments: name: string optional arguments: datatype: type ballons: string noWidgetValue: value

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NetworkNodeNetworkNodeclass ReadImage(NetworkNode): """based on the Image.open function. Reads an image file Input: filename (string) Output: Image""" def __init__(self, name='Read Image'): NetworkNode.__init__(self, name=name) self.readOnly = 1 self.inputPortsDescr.append( {'name':'filename', 'datatype':‘string’} ) self.outputPortsDescr.append( {'name':'image', 'datatype':’image’ } )

self.widgetDescr['filename'] = {'class':NEEntryWithFileBrowser, 'master':'node', 'filetypes': [('all', '*')], 'title':'read image’, 'width':10 } code = """def doit(self, filename): import Image im = Image.open(filename) if im: self.outputData(image=im)\n""" self.setFunction(code)

Widgets description: Key: port name values: class: widget class master: ‘node’ or None widget specific name:value pairs

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NetworkNodeNetworkNodeclass ReadImage(NetworkNode): """based on the Image.open function. Reads an image file Input: filename (string) Output: Image""" def __init__(self, name='Read Image'): NetworkNode.__init__(self, name=name) self.readOnly = 1 self.inputPortsDescr.append( {'name':'filename', 'datatype':‘string’} ) self.outputPortsDescr.append( {'name':'image', 'datatype':’image’ } )

self.widgetDescr['filename'] = {'class':NEEntryWithFileBrowser, 'master':'node', 'filetypes': [('all', '*')], 'title':'read image’, 'width':10 } code = """def doit(self, filename): import Image im = Image.open(filename) if im: self.outputData(image=im)\n""" self.setFunction(code)

Computational function: defined as a string set dynamically

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Node EditorNode Editor

Demo 2

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Node Libraries, data typesNode Libraries, data types

newlib = NodeLibrary(‘mylibrary’, ‘#AAEECC’)newlib.addNode(ReadImage, ‘Read Image’, ‘input’)

class ImageType(AnyType): def __init__(self): self.name = ‘image’ self.color = ‘#995699’ self.shape = ‘rect1’ def validate(self, data): import Image return isinstance(data, Image.Image)

newlib.typesTable.append( ImageType() )

Create a NodeLibraryObjectcalled ‘mylibrary’ andwith a specific color

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Node Libraries, data typesNode Libraries, data types

newlib = NodeLibrary(‘mylibrary’, ‘#AAEECC’)newlib.addNode(ReadImage, ‘Read Image’, ‘input’)

class ImageType(AnyType): def __init__(self): self.name = ‘image’ self.color = ‘#995699’ self.shape = ‘rect1’ def validate(self, data): import Image return isinstance(data, Image.Image)

newlib.typesTable.append( ImageType() )

Add a node to the library: (Class, Name, Category)

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class ImageType(AnyType): def __init__(self): self.name = ‘image’ self.color = ‘#995699’ self.shape = ‘rect1’ def validate(self, data): import Image return isinstance(data, Image.Image)

newlib.typesTable.append( ImageType() )

Node Libraries, data typesNode Libraries, data types

newlib = NodeLibrary(‘mylibrary’, ‘#AAEECC’)newlib.addNode(ReadImage, ‘Read Image’, ‘input’)

Define a new type bysubclassing AnyType.A type object providesat least a name, a colorand a shape.I can also provide avalidation function.

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Node Libraries, data typesNode Libraries, data types

newlib = NodeLibrary(‘mylibrary’, ‘#AAEECC’)newlib.addNode(ReadImage, ‘Read Image’, ‘input’)

class ImageType(AnyType): def __init__(self): self.name = ‘image’ self.color = ‘#995699’ self.shape = ‘rect1’ def validate(self, data): import Image return isinstance(data, Image.Image)

newlib.typesTable.append( ImageType() )

Add a type to alibrary of nodes.When this library isloaded the type willbe registered

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Saving NetworksSaving Networks## Network: Network 0## file written by viper## saving node Read Imagefrom ViPEr.pillib import ReadImagenode0 = ReadImage(name='Read Image’)masterNet.addNode(node0,103,57)widget = node0.inputPorts[0].widgetcfg = {}apply( widget.configure, (), cfg)if restoreWidgetValues: widget.set(‘lena.jpg’,0)## saving node Show Imagefrom ViPEr.pillib import ShowImagenode1 = ShowImage(name='Show Image')masterNet.addNode(node1, 84, 116)

## saving connections for network Network 0masterNet.connectNodes(node0, node1,0,0)

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Saving NetworksSaving Networks## Network: Network 0## file written by viper## saving node Read Imagefrom ViPEr.pillib import ReadImagenode0 = ReadImage(name='Read Image’)masterNet.addNode(node0,103,57)widget = node0.inputPorts[0].widgetcfg = {}apply( widget.configure, (), cfg)if restoreWidgetValues: widget.set(‘lena.jpg’,0)## saving node Show Imagefrom ViPEr.pillib import ShowImagenode1 = ShowImage(name='Show Image')masterNet.addNode(node1, 84, 116)

## saving connections for network Network 0masterNet.connectNodes(node0, node1,0,0)

Create a NodeLibraryObjectcalled ‘mylibrary’ andwith a specific color

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Saving NetworksSaving Networks## Network: Network 0## file written by viper## saving node Read Imagefrom ViPEr.pillib import ReadImagenode0 = ReadImage(name='Read Image’)masterNet.addNode(node0,103,57)widget = node0.inputPorts[0].widgetcfg = {}apply( widget.configure, (), cfg)if restoreWidgetValues: widget.set(‘lena.jpg’,0)## saving node Show Imagefrom ViPEr.pillib import ShowImagenode1 = ShowImage(name='Show Image')masterNet.addNode(node1, 84, 116)

## saving connections for network Network 0masterNet.connectNodes(node0, node1,0,0)

Get a handle to the widgetConfigure he widgetSet the Widget’s value

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Saving NetworksSaving Networks## Network: Network 0## file written by viper## saving node Read Imagefrom ViPEr.pillib import ReadImagenode0 = ReadImage(name='Read Image’)masterNet.addNode(node0,103,57)widget = node0.inputPorts[0].widgetcfg = {}apply( widget.configure, (), cfg)if restoreWidgetValues: widget.set(‘lena.jpg’,0)## saving node Show Imagefrom ViPEr.pillib import ShowImagenode1 = ShowImage(name='Show Image')masterNet.addNode(node1, 84, 116)

## saving connections for network Network 0masterNet.connectNodes(node0, node1,0,0)

Create second node

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Saving NetworksSaving Networks## Network: Network 0## file written by viper## saving node Read Imagefrom ViPEr.pillib import ReadImagenode0 = ReadImage(name='Read Image’)masterNet.addNode(node0,103,57)widget = node0.inputPorts[0].widgetcfg = {}apply( widget.configure, (), cfg)if restoreWidgetValues: widget.set(‘lena.jpg’,0)## saving node Show Imagefrom ViPEr.pillib import ShowImagenode1 = ShowImage(name='Show Image')masterNet.addNode(node1, 84, 116)

## saving connections for network Network 0masterNet.connectNodes(node0, node1,0,0)

Create Connectionfrom node0’s output port 0to node1’s input port 0

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Saving edited nodesSaving edited nodes

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Saving NetworksSaving Networks## Network: Network 0## file written by viper## saving node Read Imagefrom ViPEr.pillib import ReadImageclass NewNode(ReadImage): def __init__(self, name='Read Image'): apply( ReadImage.__init__, (self,), {'name':name,'originalClass':ReadImage}) code = """def doit(self, filename): print 'Reading file:', filename if filename: im = Image.open(filename)

if im: self.outputData(image=im)""" if code: self.setFunction(code) self.inputPortsDescr=[] self.outputPortsDescr=[] self.widgetDescr = {} self.inputPortsDescr.append( {'validateSrc': None, 'name': 'filename', 'balloons': None, 'required': 1, 'noWidgetValue': '', 'datatype': 'string'})

self.outputPortsDescr.append( {'balloons': None, 'name': 'image', 'datatype': 'image'}) self.widgetDescr['filename'] = { 'class': 'NEEntryWithFileBrowser', 'master': 'node'}node0 = NewNode(name='Read Image')node0.modified=1masterNet.addNode(node0,95,65)

widget = node0.inputPorts[0].widgetcfg = {}apply( widget.configure, (), cfg)if restoreWidgetValues: widget.set(”lena,jpg",0)...

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Saving NetworksSaving Networks## Network: Network 0## file written by viper## saving node Read Imagefrom ViPEr.pillib import ReadImageclass NewNode(ReadImage): def __init__(self, name='Read Image'): apply( ReadImage.__init__, (self,), {'name':name,'originalClass':ReadImage}) code = """def doit(self, filename): print 'Reading file:', filename if filename: im = Image.open(filename)

if im: self.outputData(image=im)""" if code: self.setFunction(code) self.inputPortsDescr=[] self.outputPortsDescr=[] self.widgetDescr = {} self.inputPortsDescr.append( {'validateSrc': None, 'name': 'filename', 'balloons': None, 'required': 1, 'noWidgetValue': '', 'datatype': 'string'})

self.outputPortsDescr.append( {'balloons': None, 'name': 'image', 'datatype': 'image'}) self.widgetDescr['filename'] = { 'class': 'NEEntryWithFileBrowser', 'master': 'node'}node0 = NewNode(name='Read Image')node0.modified=1masterNet.addNode(node0,95,65)

widget = node0.inputPorts[0].widgetcfg = {}apply( widget.configure, (), cfg)if restoreWidgetValues: widget.set(”lena,jpg",0)...

Subclass originalReadImage node

from ViPEr.pillib import ReadImageclass NewNode(ReadImage): def __init__(self, name='Read Image'): apply( ReadImage.__init__, (self,), {'name':name,'originalClass':ReadImage})

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Saving NetworksSaving Networks## Network: Network 0## file written by viper## saving node Read Imagefrom ViPEr.pillib import ReadImageclass NewNode(ReadImage): def __init__(self, name='Read Image'): apply( ReadImage.__init__, (self,), {'name':name,'originalClass':ReadImage}) code = """def doit(self, filename): print 'Reading file:', filename if filename: im = Image.open(filename)

if im: self.outputData(image=im)""" if code: self.setFunction(code) self.inputPortsDescr=[] self.outputPortsDescr=[] self.widgetDescr = {} self.inputPortsDescr.append( {'validateSrc': None, 'name': 'filename', 'balloons': None, 'required': 1, 'noWidgetValue': '', 'datatype': 'string'})

self.outputPortsDescr.append( {'balloons': None, 'name': 'image', 'datatype': 'image'}) self.widgetDescr['filename'] = { 'class': 'NEEntryWithFileBrowser', 'master': 'node'}node0 = NewNode(name='Read Image')node0.modified=1masterNet.addNode(node0,95,65)

widget = node0.inputPorts[0].widgetcfg = {}apply( widget.configure, (), cfg)if restoreWidgetValues: widget.set(”lena,jpg",0)...

Define modifiedcomputationalfunction

code = """def doit(self, filename): print 'Reading file:', filename if filename: im = Image.open(filename)

if im: self.outputData(image=im)""" if code: self.setFunction(code)

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Saving NetworksSaving Networks## Network: Network 0## file written by viper## saving node Read Imagefrom ViPEr.pillib import ReadImageclass NewNode(ReadImage): def __init__(self, name='Read Image'): apply( ReadImage.__init__, (self,), {'name':name,'originalClass':ReadImage}) code = """def doit(self, filename): print 'Reading file:', filename if filename: im = Image.open(filename)

if im: self.outputData(image=im)""" if code: self.setFunction(code) self.inputPortsDescr=[] self.outputPortsDescr=[] self.widgetDescr = {} self.inputPortsDescr.append( {'validateSrc': None, 'name': 'filename', 'balloons': None, 'required': 1, 'noWidgetValue': '', 'datatype': 'string'})

self.outputPortsDescr.append( {'balloons': None, 'name': 'image', 'datatype': 'image'}) self.widgetDescr['filename'] = { 'class': 'NEEntryWithFileBrowser', 'master': 'node'}node0 = NewNode(name='Read Image')node0.modified=1masterNet.addNode(node0,95,65)

widget = node0.inputPorts[0].widgetcfg = {}apply( widget.configure, (), cfg)if restoreWidgetValues: widget.set(”lena,jpg",0)...

Describe portsand widgets

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Saving NetworksSaving Networks## Network: Network 0## file written by viper## saving node Read Imagefrom ViPEr.pillib import ReadImageclass NewNode(ReadImage): def __init__(self, name='Read Image'): apply( ReadImage.__init__, (self,), {'name':name,'originalClass':ReadImage}) code = """def doit(self, filename): print 'Reading file:', filename if filename: im = Image.open(filename)

if im: self.outputData(image=im)""" if code: self.setFunction(code) self.inputPortsDescr=[] self.outputPortsDescr=[] self.widgetDescr = {} self.inputPortsDescr.append( {'validateSrc': None, 'name': 'filename', 'balloons': None, 'required': 1, 'noWidgetValue': '', 'datatype': 'string'})

self.outputPortsDescr.append( {'balloons': None, 'name': 'image', 'datatype': 'image'}) self.widgetDescr['filename'] = { 'class': 'NEEntryWithFileBrowser', 'master': 'node'}node0 = NewNode(name='Read Image')node0.modified=1masterNet.addNode(node0,95,65)

widget = node0.inputPorts[0].widgetcfg = {}apply( widget.configure, (), cfg)if restoreWidgetValues: widget.set(”lena,jpg",0)...

Create an instance ofNewNode.Remember it does notcome from a library.Add it to the network.

node0 = NewNode(name='Read Image')node0.modified=1masterNet.addNode(node0,95,65)

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Saving NetworksSaving Networks## Network: Network 0## file written by viper## saving node Read Imagefrom ViPEr.pillib import ReadImageclass NewNode(ReadImage): def __init__(self, name='Read Image'): apply( ReadImage.__init__, (self,), {'name':name,'originalClass':ReadImage}) code = """def doit(self, filename): print 'Reading file:', filename if filename: im = Image.open(filename)

if im: self.outputData(image=im)""" if code: self.setFunction(code) self.inputPortsDescr=[] self.outputPortsDescr=[] self.widgetDescr = {} self.inputPortsDescr.append( {'validateSrc': None, 'name': 'filename', 'balloons': None, 'required': 1, 'noWidgetValue': '', 'datatype': 'string'})

self.outputPortsDescr.append( {'balloons': None, 'name': 'image', 'datatype': 'image'}) self.widgetDescr['filename'] = { 'class': 'NEEntryWithFileBrowser', 'master': 'node'}node0 = NewNode(name='Read Image')node0.modified=1masterNet.addNode(node0,95,65)

widget = node0.inputPorts[0].widgetcfg = {}apply( widget.configure, (), cfg)if restoreWidgetValues: widget.set(”lena,jpg",0)...

Get a handle to widgetand configure it

widget = node0.inputPorts[0].widgetcfg = {}apply( widget.configure, (), cfg)

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Saving NetworksSaving Networks## Network: Network 0## file written by viper## saving node Read Imagefrom ViPEr.pillib import ReadImageclass NewNode(ReadImage): def __init__(self, name='Read Image'): apply( ReadImage.__init__, (self,), {'name':name,'originalClass':ReadImage}) code = """def doit(self, filename): print 'Reading file:', filename if filename: im = Image.open(filename)

if im: self.outputData(image=im)""" if code: self.setFunction(code) self.inputPortsDescr=[] self.outputPortsDescr=[] self.widgetDescr = {} self.inputPortsDescr.append( {'validateSrc': None, 'name': 'filename', 'balloons': None, 'required': 1, 'noWidgetValue': '', 'datatype': 'string'})

self.outputPortsDescr.append( {'balloons': None, 'name': 'image', 'datatype': 'image'}) self.widgetDescr['filename'] = { 'class': 'NEEntryWithFileBrowser', 'master': 'node'}node0 = NewNode(name='Read Image')node0.modified=1masterNet.addNode(node0,95,65)

widget = node0.inputPorts[0].widgetcfg = {}apply( widget.configure, (), cfg)if restoreWidgetValues: widget.set(”lena,jpg",0)...

Restore the widget’svalue only if therestoreWidgetValueoption is enabled.

if restoreWidgetValues: widget.set(”lena,jpg",0)

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MacrosMacros

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WidgetsWidgets

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Example 1:Example 1: Tomographic Tomographic reconstructionreconstruction

Image by Daniel Stoffler

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Example 2:Example 2: symmetry server symmetry server

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Future DirectionsFuture Directionso Still needs a lot of work :)

? optimization, documentation, addingfeatures

o Multi-threaded execution schedulingo Layered networkso Become Tkinter independent ?o More nodes and libraries, Web repositoryo Integration into PMVo Open Source

Michel F. SANNER TSRI 2002

ConclusionConclusion

o General Purpose VisualProgramming Environment

o Lightweight nodes / code reuseo Dynamically extensibleo Scriptable

o Used on real scientific problems

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Availability: the Availability: the packagerpackager

http://www.scripps.edu/~sanner/python

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AcknowledgmentsAcknowledgments

o Molecular Graphics Lab. at TSRIo NIH (NBCR RR08605)o Swiss National Science Foundationo Garrett M. Morris

? (“if > 5” network design)

http://www.scripps.edu/~sanner/python