PythonArithmetic¶

MLModule¶

author	`MeVis Medical Solutions AG`
package	`MeVisLab/Standard`
dll	`MLPythonImageProcessing`
definition	PythonArithmetic.def
see also	`Arithmetic`
keywords	`numpy`

Purpose¶

The module PythonArithmetic allows to implement a paged ML image calculation using Python and NumPy.

Details¶

Calculation Panel¶

This defines the implementation of the paged ML image processing (aka calculateOutputSubImage).

The following variables are predefined:

out - the output sub image that should be filled with data (representing the ML output page)

in0, in1, etc. - the input sub images (or None if it was requested from a DummyImage)

numpy - NumPy is already imported and available via as “numpy” module

constants - the variables defined in the Constants panel are available by their given name

The out and in0, in1, etc. variables are PySubImage classes (see MeVisLab Scripting Reference for the full API) which is derived from numpy.ndarray and thus supports the whole ndarray API.

For details on numpy and ndarray, see numpy and ndarray.

In addition the the above variables, all variables that are set in calculateOutputImageProperties are directly available. The out object represents the ML output sub image (aka ML page) which should be filled with the result data.

Example for modifying the existing out:

out.fill(0)

As an alternative, you can as well assign a new ndarray to out. It is required that the assigned array is of the same extent as the ML page. The datatype may be different, the data will be converted and copied to the output ML page.

Example for assigning a new array:

out = (in0 + in1)/2.

NumPy is directly available via numpy. Example for using numpy:

out = numpy.minimum(in0, in1)

Note that for debugging your code, you can simple use print on any object or dir() / help() to get the API documentation for any object.

Function Declaration¶

You cannot call other global functions in global functions, but you can use closures.

Not working example:

def bar(value):
  return value + 1
def foo(value):
  return bar(value)

print foo(1)

--> error, bar is undefined

Instead, encapsulate all functions in a closure:

def myClosure(value)
  def bar(value):
    return value + 1
  def foo(value):
    return bar(value)
  return foo(value)

function = myClosure(1)
print function

Outputs Panel¶

This allows to set the output image properties via fields or by implementing the output image property setup in Python. The default is to use copy the properties of the input image 0.

The following variables are predefined:

outImage - the output image (with writeable properties)

inImage0, inImage1, … - the input images (or None if it was requested from a DummyImage)

numpy - NumPy is already imported and available via as “numpy” module

constants - the variables defined in the Constants panel are available by their given name

Example of a custom output properties calculation:

# set datatype explicitly
outImage.setDataType(outImage.MLuint16Type)

# set page extent to the whole slice
extent = outImage.imageExtent()
outImage.setPageExtent(extent[0], extent[1], 1,1,1,1)

# set the min/max value depending on min/ax of two input images
outImage.setMinVoxelValue(min(inImage0.minVoxelValue(), inImage1.minVoxelValue()))
outImage.setMaxVoxelValue(inImage0.maxVoxelValue() +  inImage1.maxVoxelValue())

# assign an additional variable for later use in calculation
inputExtent0 = inputImage0.imageExtent()

Note that all declared variables and imported modules are automatically available in calculateOutputSubImage and calculateInputSubImageBox.

Inputs Panel¶

Allows to configure the number of inputs that are available and which data type their sub images should have. If an input is allowed to be invalid, the input sub images in the calculation will be None. It is also possible to change the input sub image boxes that are requested using Python, but this is considered an advanced feature.

The following variables are predefined:

inIndex - the output image (with writeable properties)

outBox - the box of the output page for which the input box is needed

inBox - the input box that should be requested for image at inIndex (default: None)

Constants Panel¶

Allows to set named constants that are available in Python and can be modified via scripting or field connections. Currently 6 ints and 6 doubles are supported.

If your constants do not need to be modified via fields, you should better declare them in the calculation of the output image properties.

Input Fields¶

input0¶

name: input0, type: Image¶

input1¶

name: input1, type: Image¶

input2¶

name: input2, type: Image¶

input3¶

name: input3, type: Image¶

input4¶

name: input4, type: Image¶

Output Fields¶

output0¶

name: output0, type: Image¶

Parameter Fields¶

Field Index¶

`Calculate Input Sub Image Box`: `String`	`Min Voxel Value`: `Double`
`Calculate Output Image Properties`: `String`	`setDataType`: `Bool`
`Calculate Output Sub Image`: `String`	`setMinMaxValues`: `Bool`
`Data Type`: `Enum`	`Update`: `Trigger`
`Handling`: `Enum`
`Input Type 0`: `Enum`
`Inputs`: `Integer`
`Max Voxel Value`: `Double`

Visible Fields¶

Calculate Output Sub Image¶

name: calculateOutputSubImage, type: String¶: The python code for the calculation of the output sub image.

Calculate Input Sub Image Box¶

name: calculateInputSubImageBox, type: String¶: The python code for the calculation of the input sub image box. If not implemented, the input sub image box equals the output sub image box.

Calculate Output Image Properties¶

name: calculateOutputImageProperties, type: String¶: The python code for the calculation of the output image properties.

Update¶

name: update, type: Trigger¶: Updates the output image according to all changes that have been done on the module.

Inputs¶

name: numberOfInputs, type: Integer, default: 2, minimum: 0, maximum: 5¶: Select the number of input images that the module should use.

Min Voxel Value¶

name: minVoxelValue, type: Double, default: 0¶: The minimum voxel value of the output image.

Max Voxel Value¶

name: maxVoxelValue, type: Double, default: 0¶: The maximum voxel value of the output image.

Data Type¶

name: dataType, type: Enum, default: unsigned int8¶: The data type of the output image. If this is disabled, the type of the first input image is used.

Values:

Title	Name
unsigned int8	unsigned int8
unsigned int16	unsigned int16
unsigned int32	unsigned int32
unsigned int64	unsigned int64
int8	int8
int16	int16
in32	in32
int64	int64
float	float
double	double
long double	long double
complexf	complexf
complexd	complexd
complexld	complexld

Input Type 0¶

name: inputDataType0, type: Enum, default: output type¶: Select the type of the input image 0. Default is the output type.

Values:

Title	Name	Description
output type	output type	The type of the output image.
input type	input type	The type of the input image.
unsigned int8	unsigned int8
unsigned int16	unsigned int16
unsigned int32	unsigned int32
unsigned int64	unsigned int64
int8	int8
int16	int16
in32	in32
int64	int64
float	float
double	double
long double	long double
complexf	complexf
complexd	complexd
complexld	complexld

Handling¶

name: inputHandling0, type: Enum, default: AllowAny¶: Select what the module should do when the input image is invalid.

Values:

Title	Name	Description
Invalidate	Invalidate	If the input image 0 is invalid or disconnected, just invalidate the output image.
Allow Any	AllowAny	Allow both an invalid or disconnected input image 0, make sure to check the in0 for None in your Python code, otherwise you will access the None object in case of an invalid input image.
Allow Invalid Image	AllowInvalidImage	Allow an invalid input image 0, make sure to check the in0 for None in your Python code, otherwise you will access the None object in case of an invalid input image.
Allow Disconnected Input	AllowDisconnectedInput	Allow a disconnected input image 0, make sure to check the in0 for None in your Python code, otherwise you will access the None object in case of an invalid input image.

PythonArithmetic¶

Purpose¶

Details¶

Calculation Panel¶

Function Declaration¶

Outputs Panel¶

Inputs Panel¶

Constants Panel¶

Input Fields¶

input0¶

input1¶

input2¶

input3¶

input4¶

Output Fields¶

output0¶

Parameter Fields¶

Field Index¶

Visible Fields¶

Calculate Output Sub Image¶

Calculate Input Sub Image Box¶

Calculate Output Image Properties¶

Update¶

Inputs¶

Min Voxel Value¶

Max Voxel Value¶

Data Type¶

Input Type 0¶

Handling¶

Hidden Fields¶

setMinMaxValues¶

setDataType¶

Table of Contents

PythonArithmetic¶

Purpose¶

Details¶

Calculation Panel¶

Function Declaration¶

Outputs Panel¶

Inputs Panel¶

Constants Panel¶

Input Fields¶

input0¶

input1¶

input2¶

input3¶

input4¶

Output Fields¶

output0¶

Parameter Fields¶

Field Index¶

Visible Fields¶

Calculate Output Sub Image¶

Calculate Input Sub Image Box¶

Calculate Output Image Properties¶

Update¶

Inputs¶

Min Voxel Value¶

Max Voxel Value¶

Data Type¶

Input Type 0¶

Handling¶

Hidden Fields¶

setMinMaxValues¶

setDataType¶

Table of Contents

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