From 390895d86c5e07111cf4edd1f38b01f1f3b7b505 Mon Sep 17 00:00:00 2001
From: qnater <quentin.nater@gmail.com>
Date: Fri, 27 Sep 2024 15:38:32 +0200
Subject: [PATCH] 2. adding of eeg dataset with bayesian tests

---
 .idea/workspace.xml                           |  34 +++++++-----------
 env/default_values.toml                       |   2 +-
 .../__pycache__/imputation.cpython-312.pyc    | Bin 11624 -> 11636 bytes
 imputegap/imputation/imputation.py            |   6 ++--
 .../algorithm_parameters.cpython-312.pyc      | Bin 2692 -> 2713 bytes
 .../optimization/algorithm_parameters.py      |   2 +-
 requirements.txt                              |   2 +-
 .../test_opti_bayesian_iim.cpython-312.pyc    | Bin 3523 -> 3524 bytes
 tests/test_opti_bayesian_iim.py               |   3 +-
 9 files changed, 19 insertions(+), 30 deletions(-)

diff --git a/.idea/workspace.xml b/.idea/workspace.xml
index b7b3821..0188e16 100644
--- a/.idea/workspace.xml
+++ b/.idea/workspace.xml
@@ -2,22 +2,12 @@
 <project version="4">
   <component name="ChangeListManager">
     <list default="true" id="d2565aa5-b0c7-4b53-9b23-84bd42c9e5d7" name="Changes" comment="">
-      <change afterPath="$PROJECT_DIR$/.github/workflows/pytest_opt_cdrec.yml" afterDir="false" />
-      <change afterPath="$PROJECT_DIR$/.github/workflows/pytest_opt_iim.yml" afterDir="false" />
-      <change afterPath="$PROJECT_DIR$/.github/workflows/pytest_opt_mrnn.yml" afterDir="false" />
-      <change afterPath="$PROJECT_DIR$/.github/workflows/pytest_opt_stmvl.yml" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/.github/workflows/pytest_contamination.yml" beforeDir="false" afterPath="$PROJECT_DIR$/.github/workflows/pytest_contamination.yml" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/.github/workflows/pytest_imp_cdrec.yml" beforeDir="false" afterPath="$PROJECT_DIR$/.github/workflows/pytest_imp_cdrec.yml" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/.github/workflows/pytest_imp_iim.yml" beforeDir="false" afterPath="$PROJECT_DIR$/.github/workflows/pytest_imp_iim.yml" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/.github/workflows/pytest_imp_mrnn.yml" beforeDir="false" afterPath="$PROJECT_DIR$/.github/workflows/pytest_imp_mrnn.yml" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/.github/workflows/pytest_imp_stmvl.yml" beforeDir="false" afterPath="$PROJECT_DIR$/.github/workflows/pytest_imp_stmvl.yml" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/.github/workflows/pytest_loading.yml" beforeDir="false" afterPath="$PROJECT_DIR$/.github/workflows/pytest_loading.yml" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/.github/workflows/pytest_shap_explainer.yml" beforeDir="false" afterPath="$PROJECT_DIR$/.github/workflows/pytest_shap_explainer.yml" afterDir="false" />
       <change beforePath="$PROJECT_DIR$/.idea/workspace.xml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/workspace.xml" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/README.md" beforeDir="false" afterPath="$PROJECT_DIR$/README.md" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/assets/imputegab_logo.png" beforeDir="false" afterPath="$PROJECT_DIR$/assets/logo_imputegab.png" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/imputegap/contamination/README.md" beforeDir="false" afterPath="$PROJECT_DIR$/imputegap/contamination/README.md" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/tests/test_opti_bayesian_cdrec.py" beforeDir="false" afterPath="$PROJECT_DIR$/tests/test_opti_bayesian_cdrec.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/env/default_values.toml" beforeDir="false" afterPath="$PROJECT_DIR$/env/default_values.toml" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/imputegap/imputation/imputation.py" beforeDir="false" afterPath="$PROJECT_DIR$/imputegap/imputation/imputation.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/imputegap/optimization/algorithm_parameters.py" beforeDir="false" afterPath="$PROJECT_DIR$/imputegap/optimization/algorithm_parameters.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/requirements.txt" beforeDir="false" afterPath="$PROJECT_DIR$/requirements.txt" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/tests/test_opti_bayesian_iim.py" beforeDir="false" afterPath="$PROJECT_DIR$/tests/test_opti_bayesian_iim.py" afterDir="false" />
     </list>
     <option name="SHOW_DIALOG" value="false" />
     <option name="HIGHLIGHT_CONFLICTS" value="true" />
@@ -79,7 +69,7 @@
       <recent name="C:\Users\nquen\switchdrive\MST_MasterThesis\imputegap\assets" />
     </key>
   </component>
-  <component name="RunManager" selected="Python tests.Python tests in test_opti_bayesian_cdrec.py">
+  <component name="RunManager" selected="Python tests.Python tests in test_opti_bayesian_iim.py">
     <configuration name="runner_imputation" type="PythonConfigurationType" factoryName="Python" temporary="true" nameIsGenerated="true">
       <module name="imputegap" />
       <option name="INTERPRETER_OPTIONS" value="" />
@@ -154,7 +144,7 @@
       <option name="_new_targetType" value="&quot;PATH&quot;" />
       <method v="2" />
     </configuration>
-    <configuration name="Python tests in tests" type="tests" factoryName="Autodetect" temporary="true" nameIsGenerated="true">
+    <configuration name="Python tests in test_opti_bayesian_iim.py" type="tests" factoryName="Autodetect" temporary="true" nameIsGenerated="true">
       <module name="imputegap" />
       <option name="INTERPRETER_OPTIONS" value="" />
       <option name="PARENT_ENVS" value="true" />
@@ -165,7 +155,7 @@
       <option name="ADD_SOURCE_ROOTS" value="true" />
       <EXTENSION ID="PythonCoverageRunConfigurationExtension" runner="coverage.py" />
       <option name="_new_additionalArguments" value="&quot;&quot;" />
-      <option name="_new_target" value="&quot;$PROJECT_DIR$/tests&quot;" />
+      <option name="_new_target" value="&quot;$PROJECT_DIR$/tests/test_opti_bayesian_iim.py&quot;" />
       <option name="_new_targetType" value="&quot;PATH&quot;" />
       <method v="2" />
     </configuration>
@@ -173,16 +163,16 @@
       <item itemvalue="Python.runner_imputation" />
       <item itemvalue="Python.runner_optimization" />
       <item itemvalue="Python tests.Python tests in test_opti_bayesian_cdrec.py" />
+      <item itemvalue="Python tests.Python tests in test_opti_bayesian_iim.py" />
       <item itemvalue="Python tests.Python tests in test_explainer.py" />
-      <item itemvalue="Python tests.Python tests in tests" />
     </list>
     <recent_temporary>
       <list>
+        <item itemvalue="Python tests.Python tests in test_opti_bayesian_iim.py" />
         <item itemvalue="Python tests.Python tests in test_opti_bayesian_cdrec.py" />
         <item itemvalue="Python.runner_imputation" />
         <item itemvalue="Python.runner_optimization" />
         <item itemvalue="Python tests.Python tests in test_explainer.py" />
-        <item itemvalue="Python tests.Python tests in tests" />
       </list>
     </recent_temporary>
   </component>
@@ -211,7 +201,7 @@
       <workItem from="1727357029326" duration="44000" />
       <workItem from="1727358317602" duration="1867000" />
       <workItem from="1727361217072" duration="594000" />
-      <workItem from="1727434411640" duration="8444000" />
+      <workItem from="1727434411640" duration="8803000" />
     </task>
     <servers />
   </component>
@@ -235,7 +225,7 @@
     <SUITE FILE_PATH="coverage/imputegap$test.coverage" NAME="test Coverage Results" MODIFIED="1727099350719" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$" />
     <SUITE FILE_PATH="coverage/imputegap$test__1_.coverage" NAME="test (1) Coverage Results" MODIFIED="1727099954120" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$/imputegap" />
     <SUITE FILE_PATH="coverage/imputegap$_loading.coverage" NAME="_loading Coverage Results" MODIFIED="1726134442146" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$/imputegap/loading" />
-    <SUITE FILE_PATH="coverage/imputegap$.coverage" NAME=" Coverage Results" MODIFIED="1727443305357" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$/tests" />
+    <SUITE FILE_PATH="coverage/imputegap$.coverage" NAME=" Coverage Results" MODIFIED="1727444189590" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$/tests" />
     <SUITE FILE_PATH="coverage/imputegap$runner_optimization.coverage" NAME="runner_optimization Coverage Results" MODIFIED="1727437737184" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$/imputegap" />
     <SUITE FILE_PATH="coverage/imputegap$runner_imputation.coverage" NAME="runner_imputation Coverage Results" MODIFIED="1727439213786" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$/imputegap" />
   </component>
diff --git a/env/default_values.toml b/env/default_values.toml
index 618eb45..877848a 100644
--- a/env/default_values.toml
+++ b/env/default_values.toml
@@ -10,7 +10,7 @@ gamma = 0.85
 alpha = 7
 
 [iim]
-neighbor = 10
+learning_neighbors = 10
 algorithm_code = "iim 2"
 
 [mrnn]
diff --git a/imputegap/imputation/__pycache__/imputation.cpython-312.pyc b/imputegap/imputation/__pycache__/imputation.cpython-312.pyc
index 9bc19cbc5836514348b6da2ba3be0edd5b186fa5..734397fe7b1767a802198d7be26f907d522b57a0 100644
GIT binary patch
delta 1038
zcmaD6^(Bh;G%qg~0}!0u@-6MqM&3JY!a_NziA8ytdFk<ashQ~+N%=*^n?JG1F|rm(
z0M$*F<~YFkZ1WusJw|Osl?7odTo=Y(Fm}JF>Ty}o^8%0D4GFm!r89XisF_`qFz@iZ
zA*QiH^Ma_!W@D~;Hb#TZn*~;~FxpR!6_sK%oLnKQ%4P>Nv&eq(Vo^IrgUOFXr!aa=
zE*CS=@&XAPfCv*1;R7TRf%r2!kZ57}!X(0}T?AHRGTBf~a`QW}b|!6qpxjE<B8Z7V
zc9AZK2mld*K%$rxNGO0nk-_8zk|``8{geA-#Wu@H1u=<&bQeXVt80}>jt1Kk1eDQa
zEeZyy3IP$JAc7M_uz`p$5CM1fE!N<Y#FFBoNT6s15Et_Ri57;>OnjW$Ulf1@L}@J0
z@g|$gW%o1H`vDbbG8fqcsayPcrMXF|Mey)1(g#Vh7J&>YG6WGIuM}~C2#~Wi+0i_G
zixVDoV7*9z017~GAb^4aWPk;bs8X4{UZL9q;ZYWJkAhU8`LW0xBo+@OW`P*tAOdWH
zIoMa*6or^Mz`kMy#_t6cc^R<FLG~lLoD=Hu$=s^4a)_t`g)7vRFn3x_c2ix9&xuwb
zlTo9g$Py%$0wgwq7zig?ZZ=dq40Rq0(0P9}r2@gu;{d5c1S|(yz!r&u<i$XQIEX;F
z7^D&AVo1Q+OitIDZh$9DZ9pcVIoNu#p0*?#Sd;Z+Uu_9nv;+rsq$fxtIA6qqSm1a7
m`_vlE#L0`aBY44vfs&4<P?70ob{%#`ZX`=5OX_-qa{>Uz5zajT

delta 1073
zcmaKrOH30{6oxy~*R-`r#15_YMM6oY6|{s_9#Xp^VuKIxL8?JP5RHO*+a|^YyTNE;
zf{SY+xWbqayD=fNa;5A{+(6uzhJ_0k>}_1R@cg%oEnP6ld~@$PXYT#ae`hM$ovizt
z+wC;bb^qO;+iUCYZJR@xpSe4GXX*jd|Js6*tL!l5IUZ8JNWb)-N|&U0k1h|bCRRp1
zM7R8j@80B#;UC`Ma$&{2*^%7xo}{T7TJ>#uVtSvmXp`dlr{<EypQfEy7vKk42%420
zz_^<~^+ar^F--H4Cnd%Cj_0+M;R|X{a|Yo!kN`&bhI-g0f(gFV=F=<cb2)Z_QY9;^
zE`hR6;36<e$XN+tTrAGleA7}!cOAJWd+-{&-dOO`f9smqV2m=P@e-;o16KeCU<0lK
z|MiuvWBJK^j%6wOnC={UTQvQan;fx9m{2X9Ak{tkLg2GpJWmChnWgDbJ~&^Po0?%a
z49D3CBn^XT%+LeFficL|?2X+XM+$G%^=+rA=o_6Q)kk>JK0NoZke}om;b&)RjanKT
zMQuZmtQWDHgtr)s17d|<eW`88tcZ@Rbc);UA%8crP*A7Zv8$T5Mgqaw`M}d%orcl@
zJ{ozypS%IAy!QxLKVs8_bqs3q`i1F_I$oJmLZU^O&OE46fmXsEw-rQdZYzfFRMZ=&
z=|+{IyK3+t&qd!9_i=R)3pdC<h1e|NE8RI*wrHxzs`1GneNK~E6Fr#)FcUOq<ADjo
t&r&K<{Z}SXDo#xJB6g|UnSYFpyM<DGsoEiy)LV|(C0Bh(q%&hd$v?<;&vpO+

diff --git a/imputegap/imputation/imputation.py b/imputegap/imputation/imputation.py
index 79603de..727ddb8 100644
--- a/imputegap/imputation/imputation.py
+++ b/imputegap/imputation/imputation.py
@@ -32,7 +32,7 @@ def load_parameters(query="default", algorithm="cdrec"):
         if not os.path.exists(filepath):
             filepath = filepath[:1]
 
-        with open(filepath, "r") as file:
+        with open(filepath, "r") as _:
             config = toml.load(filepath)
 
         params = None
@@ -47,9 +47,9 @@ def load_parameters(query="default", algorithm="cdrec"):
             alpha = int(config['stmvl']['alpha'])
             params = (window_size, gamma, alpha)
         elif algorithm == "iim":
-            neighbors = int(config['iim']['neighbor'])
+            learning_neighbors = int(config['iim']['learning_neighbors'])
             algo_code = config['iim']['algorithm_code']
-            params = (neighbors, algo_code)
+            params = (learning_neighbors, algo_code)
         elif algorithm == "mrnn":
             hidden_dim = int(config['mrnn']['hidden_dim'])
             learning_rate = float(config['mrnn']['learning_rate'])
diff --git a/imputegap/optimization/__pycache__/algorithm_parameters.cpython-312.pyc b/imputegap/optimization/__pycache__/algorithm_parameters.cpython-312.pyc
index 2d874f2921c0a8983fac38b38c6305649cf27fd2..72f742a745158488b41796275dca7c6db256d1a9 100644
GIT binary patch
delta 132
zcmZn>ohizDnwOW00SKmT`IfeKBX1hBrg}PKIzx)aA`q#$h%rTR4oj3MkgWw|GlS){
z!E!p2=P*Yz>TdqQJd;u6mQYS=Vo_dZUV409YG!&yQhrhK<cX~DjOv>|vi@S^vIknh
X2*kyao4>MiGqEUK;8vW>%+&}08=NN?

delta 110
zcmbO!+9Jw(nwOW00SL~n`j)nNBX1hBrdT>-Izx*3A`q#uh%rTR4oj3MkgW-1GlS){
zz;fD?=P*Yz>TLeOJd<(qQr37zwau(-zZkjffTl45adE_EP7ZD+X0Z;N$r4<R0GM4I
A!2kdN

diff --git a/imputegap/optimization/algorithm_parameters.py b/imputegap/optimization/algorithm_parameters.py
index 7fb8cf1..f186373 100644
--- a/imputegap/optimization/algorithm_parameters.py
+++ b/imputegap/optimization/algorithm_parameters.py
@@ -42,7 +42,7 @@
 # Define the parameter names for each algorithm
 PARAM_NAMES = {
     'cdrec': ['rank', 'epsilon', 'iteration'],
-    'iim': ['neighbor'],
+    'iim': ['learning_neighbors'],
     'mrnn': ['hidden_dim', 'learning_rate', 'iterations', 'seq_len' ],
     'stmvl': ['window_size', 'gamma', 'alpha']
 }
diff --git a/requirements.txt b/requirements.txt
index a873ff3..1c9e028 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,4 @@
-numpy==1.13.3
+numpy==1.21.5
 pandas==2.0.3
 matplotlib==3.7.5
 toml==0.10.2
diff --git a/tests/__pycache__/test_opti_bayesian_iim.cpython-312.pyc b/tests/__pycache__/test_opti_bayesian_iim.cpython-312.pyc
index efdcba2667a0d78c3dfa930bfc0978f2068c8c4d..f189be83a58c4bb260cc42f509b341c995d0af8e 100644
GIT binary patch
delta 85
zcmX>seMFk~G%qg~0}v!^`Ict1k#{c_qyOa7T*oHw=Vlf5VY(pe_?dx0&X?&Thg1h+
nhy9(&E4WWEN^dUYv1JsMWmKD>aa~CHqLA`e1|X+M0B8;Xigp=A

delta 88
zcmX>ieOQ|JG%qg~0}v#x`j(cmk#{c_qu=DyT*t(2Sh#&)W{`7Y{LH{8=fQZ9L#l(Z
q!+vrlx9sGj+-n$RHW%^OGK$JEs!h<iE~I=>Nck%RkW(Z8GztL9%o&sb

diff --git a/tests/test_opti_bayesian_iim.py b/tests/test_opti_bayesian_iim.py
index 69639c0..2d49dcd 100644
--- a/tests/test_opti_bayesian_iim.py
+++ b/tests/test_opti_bayesian_iim.py
@@ -55,8 +55,7 @@ def test_optimization_bayesian_stmvl(self):
         params = Imputation.load_parameters(query="default", algorithm=algorithm)
         params_optimal = (optimal_params['neighbor'], "iim 2")
 
-        _, metrics_optimal = Imputation.Regression.iim_imputation(ground_truth=gap.ts, contamination=ts_contaminated,
-                                                 params=params_optimal)
+        _, metrics_optimal = Imputation.Regression.iim_imputation(ground_truth=gap.ts, contamination=ts_contaminated, params=params_optimal)
         _, metrics_default = Imputation.Regression.iim_imputation(ground_truth=gap.ts, contamination=ts_contaminated, params=params)
 
         Optimization.save_optimization(optimal_params=optimal_params, algorithm=algorithm+"_test")