Remove Block #15

jialuw96 · 2023-02-07T20:28:09Z

Fixes # .

Summary/Motivation:

Changes proposed in this PR:

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jialuw96 · 2023-02-07T20:30:40Z

@adowling2 I still cannot add reviewers.

adowling2

@jialuw96 Here are some comments. The import statements look strange. We can talk about this on Friday.

Once the interface is changed and the examples are updated, we need to write unit tests for new features. For instance, we are changing the interface to the Measurement class. We should write unit tests for that.

adowling2 · 2023-02-09T11:24:36Z

pyomo/contrib/doe/doe.py

-from pyomo.contrib.doe.result import FisherResults, GridSearchResult
+#from pyomo.contrib.doe.scenario import Scenario_generator
+#from pyomo.contrib.doe.result import FisherResults, GridSearchResult
+from scenario import Scenario_generator


Why is this missing pyomo.contrib.doe at the beginning of the import statement? Happy to discuss in detail on Friday.

pyomo/contrib/doe/doe.py

adowling2 · 2023-02-09T11:33:32Z

pyomo/contrib/doe/example/reactor_kinetics.py

@@ -29,44 +29,45 @@
 import pyomo.environ as pyo
 from pyomo.dae import ContinuousSet, DerivativeVar
 import numpy as np
-from pyomo.contrib.doe import Measurements
+from measurements import Measurements


Why did this import statement change? We can discuss on Friday.

pyomo/contrib/doe/measurements.py

jialuw96 · 2023-02-12T19:53:48Z

@adowling2 The compute_fim() function is ready for review, both sequential_finite mode and direct_kaug mode. scenario and measurement class and the reactor kinetics example are also updated per discussion. Thank you!

adowling2

@jialuw96 See my comments.

adowling2 · 2023-02-13T21:56:41Z

pyomo/contrib/doe/doe.py

-        FIM_analysis = FisherResults(list(self.param.keys()), self.measure, jacobian_info=None, all_jacobian_info=jac,
-                                    prior_FIM=prior_in_use, store_FIM=self.FIM_store_name, scale_constant_value=self.scale_constant_value)
+            # force all design variables in blocks be the same as global design variables
+            def fix_design1(m,s):


This needs to be generalized. Happy to talk about that in our next meeting. One idea is for the user to provide a list of the design variable names.

We need to think about how to do this in a way that accommodates extra indices.

pyomo/contrib/doe/doe.py

adowling2 · 2023-02-13T22:09:04Z

pyomo/contrib/doe/example/reactor_kinetics.py

-        m.index1 = False
-    elif model_form == 'dae-index-1':
-        m.index1 = True 
+    if model_option == "parmest":


Should this be...
if model_option == "parmest":
...
elif model_option == "global":
else:
if not mod:
raise error here?

This depends on if we want to create the model by ourself, or let user create model in global mode. Which one you think is better?

I think we want to do some error checking to ensure the options passed to model_option are valid.

You can resolve this discussion thread.

We do need to test these value errors are being thrown.

adowling2 · 2023-02-13T22:12:17Z

pyomo/contrib/doe/measurements.py

-        self.flatten_measure_timeset = flatten_measure_timeset
-
-    def _model_measure_name(self):
+        if self_define_res:


This is not the interface we discussed. We worked out having an add_measurement function that the user would call for each measurement and specify indices. This function would then build up the data stored in self.measurement_name.

adowling2 · 2023-02-13T22:15:00Z

pyomo/contrib/doe/measurements.py

+        else:
+            raise AttributeError("No measurement names provided. Define either self_define_res or measurement_var.")
+
+    def _measure_name(self):
        """Return pyomo string name


This doc string needs more explanation. The structure of self.measure_varname and other data are not clear.

adowling2 · 2023-02-13T22:17:17Z

pyomo/contrib/doe/measurements.py

-                    values are a list of measuring time point.
-            For e.g., for the kinetics illustrative example, it should be {'C':{'CA':[0,1,..], 'CB':[0,2,...]}, 'k':[0,4,..]},
-            so the measurements are C[scenario, 'CA', 0]..., k[scenario, 0]....
+        self_define_res: a ``list`` of ``string``, containing the measurement variable names with indexs, 


This should be split into two functions instead of having all of these optional arguments. One function to directly specify the list of all measurement variable names. The section function to build up this list. That will make the documentation and examples much clearer. It will also be easier to test.

adowling2 · 2023-02-13T22:18:07Z

pyomo/contrib/doe/result.py

@@ -85,7 +85,7 @@ def __init__(self, para_name, measure_object, jacobian_info=None, all_jacobian_i
        self.logger.setLevel(level=logging.WARN)


-    def calculate_FIM(self, dv_values, result=None):
+    def calculate_FIM(self, dv_values, black_box_res=True, result=None):


Doc string needs to be updated to explain black_box_res option.

jialuw96 · 2023-02-20T19:33:25Z

@adowling2 Optimization function is ready for review. The discussed class is in specialSet.py. Thank you!

adowling2

@jialuw96 See my comments below. Nice work!

pyomo/contrib/doe/doe.py

adowling2 · 2023-02-21T01:39:15Z

pyomo/contrib/doe/example/reactor_kinetics.py

-        for t in m.t:
-            m.dCdt_rule[z,'CC',t].deactivate()
+    if block:
+        for s in range(8):


Why is this eight hardcoded?

Still need to update.

Use len(m.block)

adowling2 · 2023-02-21T01:40:44Z

pyomo/contrib/doe/example/reactor_kinetics.py

-        m.index1 = False
-    elif model_form == 'dae-index-1':
-        m.index1 = True 
+    if model_option == "parmest":


I think we want to do some error checking to ensure the options passed to model_option are valid.

pyomo/contrib/doe/example/reactor_kinetics.py

pyomo/contrib/doe/measurements.py

jialuw96 · 2023-02-27T04:23:55Z

@adowling2 The grid search functions and variances are ready for review. Thank you!

adowling2

Please are some comments to discuss today.

pyomo/contrib/doe/doe.py

adowling2 · 2023-02-28T16:00:38Z

pyomo/contrib/doe/doe.py

            """
-            return m.FIM[j,d] == sum(sum(m.jac[z,j,i]*m.jac[z,d,i] for z in m.y_set) for i in m.tmea_set) + m.refele[j, d]*self.fim_scale_constant_value
+            return m.fim[p,q] == sum(m.jac[p,n]*m.jac[q,n] for n in mod.res) + m.priorFIM[p,q]*self.fim_scale_constant_value 


We still need to discuss this.

J.W.: work in progress

pyomo/contrib/doe/doe.py

adowling2 · 2023-02-28T16:01:58Z

pyomo/contrib/doe/example/reactor_kinetics.py

-        for t in m.t:
-            m.dCdt_rule[z,'CC',t].deactivate()
+    if block:
+        for s in range(8):


Still need to update.

Use len(m.block)

jialuw96 · 2023-02-28T19:14:08Z

variance for optimization
jacobian subset
Tictoctoker timer
try enum https://docs.python.org/3/library/enum.html
design variable class
@adowling2 This is ready to review. Thank you!

adowling2

Here are my comments. Next time this is ready to review, tag me in a new post. When you edit an existing comment, I do not always get an update.

pyomo/contrib/doe/doe.py

pyomo/contrib/doe/measurements.py

pyomo/contrib/doe/specialSet.py

jialuw96 · 2023-03-07T18:41:13Z

Enum interface update
Update tutorial notebook, documentation
Update tests

...and standardize the order of argument processing, plus remove the automatic optimization of f(.)**0 -> 1.

because Pyomo requires Python >= 3.7.

[DOC] Remove instructions for python <= 3.0

…ependencies

mod in doc string

adowling2 reviewed Feb 9, 2023

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adowling2 mentioned this pull request Feb 9, 2023

Pyomo.DoE Development Plan Pyomo/pyomo#2610

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adowling2 reviewed Feb 13, 2023

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adowling2 reviewed Mar 6, 2023

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jsiirola and others added 18 commits March 15, 2023 09:01

Remove unreachable code, add missing call to value()

f512378

changes before switching branches

83f0bb1

Finishing the paraboloid tests for the reduced inner repn transformation

997c6a2

Remove unnecessary override

5544d5c

Fix calculation of polynomial_degree(f(.)**0)

4b62c6d

Add optional optimizations for 0 in expression trees

fe7fa3c

...and standardize the order of argument processing, plus remove the automatic optimization of f(.)**0 -> 1.

Add tests for the 'zero' expression optimizations

7c5a21f

Check that all native_numeric_types are hashable

18162a0

NFC: improve docs

d9db244

NFC: fix typo, remove commented code

05e596a

Improve performance of LinearExpression.__init__

8c3094e

Switch AMPLRepn.linear from list to dict

a1a642f

Performance: faster printing of defined variables

37efae5

fix iteration over dict generators

5bf835d

Fix typo

e9580de

Improve diff reporting (report actual baseline filename)

1a53654

Add the option to build againse pyomo-model-libraries branch

ef603a5

Fix checkout of pyomo-model-libraries branch

9ef1c0d

jialuw96 and others added 30 commits May 1, 2023 23:51

added test. passed all test.

2f66d02

updated document

9e0d148

[DOC] Remove instructions for python <= 3.0

f933344

because Pyomo requires Python >= 3.7.

Adding blank line removed from doctest by mistake

6ef55c7

Merge pull request Pyomo#2822 from MLopez-Ibanez/patch-1

2b51e1c

[DOC] Remove instructions for python <= 3.0

addressing comments. pass tests

63dac55

finish updating enum. passed all tests

4844b6a

addressing comments. passed all tests.

bdabd70

scenario dictionary changed to named tuple.

7ea0a2f

Merge branch 'main' into Feb_block_doe

edaefea

update doc and notebook

c02deae

run black

e9d7b35

checked spells, fix some errors in documentation

fd60577

delete non-used numpy import; try to import numpy from pyomo.common.d…

a29f541

…ependencies

skip numpy if not numpy_available in tests

88524be

run black

1c035c3

update doe.rst according to comments

0e2922a

solve calculate_FIM() issue, rename to result_analysis, change the input

b5d7ef0

before try context manager

0b063a4

use context manager. run black

a9ea539

finish change fim_doe_tutorials

4b1e49e

fix typo

d3cb944

NFC: Fixing Sphinx warnings and docstring formatting

b1ede4c

NFC: Fix black formatting

1aa4d81

NFC: Updates to doe.rst

8312ac3

Removing unused comment

0986950

Address model Pyomo.DoE review comments

e4f46f0

mod in doc string

Added missing m: Pyomo model from doc string

0262868

Fix black formatting error?

1f61bee

Fixed variable name typo

5c0405a

Provide feedback

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Remove Block #15

Remove Block #15

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Remove Block #15

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jialuw96 commented Feb 7, 2023

Fixes # .

Summary/Motivation:

Changes proposed in this PR:

Legal Acknowledgement

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