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Add pipeline cookbook #4323

Merged

vigsterkr merged 7 commits into shogun-toolbox:feature/transformers from vinx13:meta/pipeline

Jun 28, 2018

Contributor

vinx13 commented Jun 2, 2018 •

edited

add pipeline meta example and cookbook
add transformer factory

vinx13 referenced this pull request Jun 2, 2018

Merged

Add pipeline integraton data #157

karlnapf reviewed Jun 4, 2018

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doc/cookbook/source/examples/pipeline/pipeline.rst Outdated

  
        Pipeline

        ========

        Pipeline is a machine that chains multiple transformers and machines. It consists of a sequence of transformers as intermediate stages and a machine as the final stage. Features are transformed by transformers and fed into the next stage sequentially.

karlnapf Jun 4, 2018

Member

maybe add sgclass to link to the API docs

karlnapf reviewed Jun 4, 2018

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doc/cookbook/source/examples/pipeline/pipeline.rst Outdated

  
        Pipeline

        ========

        Pipeline is a machine that chains multiple transformers and machines. It consists of a sequence of transformers as intermediate stages and a machine as the final stage. Features are transformed by transformers and fed into the next stage sequentially.

karlnapf Jun 4, 2018

Member

could you start every sentence in a new line? I.e. newline after each ".", this makes subsequent diffs way easier to review

karlnapf reviewed Jun 4, 2018

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doc/cookbook/source/examples/pipeline/pipeline.rst Outdated

  
        Pipeline

        ========

        Pipeline is a machine that chains multiple transformers and machines. It consists of a sequence of transformers as intermediate stages and a machine as the final stage. Features are transformed by transformers and fed into the next stage sequentially.

karlnapf Jun 4, 2018

Member

"stage" of what? Maybe add "stage of training"

karlnapf reviewed Jun 4, 2018

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doc/cookbook/source/index.rst

  
        .. toctree::

            :maxdepth: 1

            :glob:

karlnapf Jun 4, 2018

Member

+1

karlnapf reviewed Jun 4, 2018

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examples/meta/src/pipeline/pipeline.sg

  
        # additional integration variables

        #![extract_centers_and_radius]

        RealMatrix c = kmeans.get_cluster_centers()

karlnapf Jun 4, 2018

Member

can this be done with the generic get?

vinx13 Jun 4, 2018

Contributor

no, this is not a parameter :(

karlnapf Jun 4, 2018

Member

I see.
Ok, one of the next things I want to do is to register callback functions with get so that we can lazily evaluate things, like in this case

karlnapf reviewed Jun 4, 2018

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src/shogun/machine/Pipeline.cpp Outdated

  
        		REQUIRE(

        		    m_stages.empty() ||

        		        holds_alternative<CTransformer*>(m_stages.back()),

        		    "Transformers can not be placed after machines.\n");

karlnapf Jun 4, 2018

Member

Could you maybe make this "Last element in pipeline is %s", and then put the machine name there?

karlnapf reviewed Jun 4, 2018

View changes

src/shogun/machine/Pipeline.cpp Outdated

  
        		REQUIRE(

        		    m_stages.empty() ||

        		        holds_alternative<CTransformer*>(m_stages.back()),

        		    "Multiple machines are added to pipeline.\n");

karlnapf Jun 4, 2018

Member

same story, pls print the name of the last added machine so the user knows what she did wrong

karlnapf reviewed Jun 4, 2018

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src/shogun/machine/Pipeline.cpp Outdated

  
        	{

        		REQUIRE(

        		    !m_stages.empty() && holds_alternative<CMachine*>(m_stages.back()),

        		    "Machine has not been added.\n");

karlnapf Jun 4, 2018

Member

Could you be more elaborate here as well
"Pipline cannot be trained without an added machine. Last element is %s"

karlnapf reviewed Jun 4, 2018

View changes

src/shogun/machine/Pipeline.cpp Outdated

  
        	CLabels* CPipeline::apply(CFeatures* data)

        	{

        		REQUIRE(

        		    !m_stages.empty() && holds_alternative<CMachine*>(m_stages.back()),

karlnapf Jun 4, 2018

Member

as above. user facing error messages need to be more explicit

karlnapf reviewed Jun 4, 2018

View changes

src/shogun/machine/Pipeline.cpp Outdated

  
        	{

        		REQUIRE(

        		    !m_stages.empty() && index < m_stages.size() - 1,

        		    "Index out of bound. There are only %d transformers.\n",

karlnapf Jun 4, 2018

Member

print the index as well
"Requested index (%d) out of bounds " ...

karlnapf reviewed Jun 4, 2018

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src/shogun/machine/Pipeline.h Outdated

  
        namespace shogun

        {

        	class CPipeline : public CMachine

karlnapf Jun 4, 2018

Member

Could you write some minimal class docs?

karlnapf reviewed Jun 4, 2018

View changes

tests/unit/machine/Pipeline_unittest.cc Outdated

  
        	EXPECT_EQ(pipeline->get_transformer(1), transformer2.get());

        	EXPECT_EQ(pipeline->get_machine(), machine.get());

        }

karlnapf Jun 4, 2018

Member

great set of tests!

karlnapf reviewed Jun 4, 2018

View changes

Great work!
I made some comments on user facing parts of this

vigsterkr force-pushed the shogun-toolbox:feature/transformers branch 2 times, most recently from `b7d2ff9` to `f211b65` Jun 4, 2018

vigsterkr force-pushed the shogun-toolbox:feature/transformers branch from `f211b65` to `0fa4faa` Jun 11, 2018

vinx13 added some commits Jun 2, 2018


      Add transformer factory

f729cf0


      Add pipeline cookbook

c6e65ad

vinx13 force-pushed the vinx13:meta/pipeline branch from `f8e42ff` to `c6e65ad` Jun 13, 2018


      Update integration data

fd85b08

vigsterkr requested changes Jun 13, 2018

View changes

examples/meta/src/pipeline/pipeline.sg Outdated

  
        #![create_pipeline]

        Pipeline pipeline()

        pipeline.with(subMean)

vigsterkr Jun 13, 2018

Member

this needs fixing, because of reserved keyword

examples/meta/src/pipeline/pipeline.sg Outdated

  
        #![create_pipeline]

        Pipeline pipeline()

        pipeline.with(subMean)

        pipeline.with(pca)

vigsterkr Jun 13, 2018

Member

change it

vinx13 added some commits Jun 14, 2018


      Update pipeline cookbook to new api

dab5513


      Fix typo

a8374ce


      Init random with fixed seed

c7957b0

Member

vigsterkr commented Jun 14, 2018

pipeline.cs(31,1): error CS0246: The type or namespace name `PipelineBuilder' could not be found. Are you missing an assembly reference?
pipeline.cs(32,1): error CS0841: A local variable `builder' cannot be used before it is declared
pipeline.cs(33,1): error CS0841: A local variable `builder' cannot be used before it is declared
pipeline.cs(34,1): error CS0246: The type or namespace name `Pipeline' could not be found. Are you missing an assembly reference?
pipeline.cs(38,1): error CS0841: A local variable `pipeline' cannot be used before it is declared
pipeline.cs(39,25): error CS0841: A local variable `pipeline' cannot be used before it is declared
Compilation failed: 6 error(s), 0 warnings```

Member

vigsterkr commented Jun 14, 2018

and in java

[ 97%] Generating pipeline/pipeline.class
/opt/shogun/build/examples/meta/java/pipeline/pipeline.java:12: error: cannot find symbol
import org.shogun.Pipeline;
                 ^
  symbol:   class Pipeline
  location: package org.shogun
/opt/shogun/build/examples/meta/java/pipeline/pipeline.java:13: error: cannot find symbol
import org.shogun.PipelineBuilder;
                 ^
  symbol:   class PipelineBuilder
  location: package org.shogun
/opt/shogun/build/examples/meta/java/pipeline/pipeline.java:51: error: cannot find symbol
PipelineBuilder builder = new PipelineBuilder();
^
  symbol:   class PipelineBuilder
  location: class pipeline
/opt/shogun/build/examples/meta/java/pipeline/pipeline.java:51: error: cannot find symbol
PipelineBuilder builder = new PipelineBuilder();
                              ^
  symbol:   class PipelineBuilder
  location: class pipeline
/opt/shogun/build/examples/meta/java/pipeline/pipeline.java:54: error: cannot find symbol
Pipeline pipeline = builder.then(kmeans);
^
  symbol:   class Pipeline
  location: class pipeline
5 errors
examples/meta/java/CMakeFiles/java-pipeline-pipeline.dir/build.make:62: recipe for target 'examples/meta/java/pipeline/pipeline.class' failed
make[2]: *** [examples/meta/java/pipeline/pipeline.class] Error 1
CMakeFiles/Makefile2:5049: recipe for target 'examples/meta/java/CMakeFiles/java-pipeline-pipeline.dir/all' failed
make[1]: *** [examples/meta/java/CMakeFiles/java-pipeline-pipeline.dir/all] Error 2
Makefile:160: recipe for target 'all' failed
make: *** [all] Error 2```


      Fix swig include

56acfd9

vigsterkr merged commit `550639e` into shogun-toolbox:feature/transformers Jun 28, 2018
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vigsterkr added a commit that referenced this pull request Jun 28, 2018


      Add pipeline cookbook (#4323)

* Add transformer factory
* Add pipeline cookbook
* Fix swig include

af8af72

vigsterkr added a commit that referenced this pull request Jul 10, 2018


      Add pipeline cookbook (#4323)

* Add transformer factory
* Add pipeline cookbook
* Fix swig include

77a9f85

vigsterkr added a commit that referenced this pull request Jul 10, 2018


      Add pipeline cookbook (#4323)

* Add transformer factory
* Add pipeline cookbook
* Fix swig include

8711ea6

vigsterkr added a commit that referenced this pull request Jul 12, 2018


      Add pipeline cookbook (#4323)

* Add transformer factory
* Add pipeline cookbook
* Fix swig include

1ac4765

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