♻️ Refactor with project API (#4)

This change refactors the case studies to use the project API and did lead to some[ improvements in the project API
itself](glotaran/pyglotaran#1257).

In addition, it cleans up the model and parameter files as well as notebooks.
Further improvements like using glotaran generated clp guides and explaining the smoothing due `clp_relations` will follow in a different PR.

### Change summary

- [🧹 Add project anchor files to git
ignore](75fd1ce)
- [♻️ Moved original data files from data subfolder to
measured_data](2ec5a1c)
- [🧹 Added data folder to gitignore since it gets populated by
import_data](467fd91)
- [♻️ Converted target_rc to project
API](0701661)
- [♻️ Converted target_rcg_compare to project
API](01ba768)
- [♻️ Converted target_rcg_gcrcg_rcgcr_refine to project
API](49b92c9)
- [♻️ Moved original data 4TT files from data subfolder to
measured_data](bd06310)
- [👌 Added clp_relations for smoothong of generated guidance
spectra](cc60ac0)
- [🧹 Cleaned rcg_refine models and parameters from unused
code](524af94)
- [🧹 Removed dead code comments in target_rc
model](a88cd8c)
- [👌 Use result create_clp_guide_dataset method instead of
function](84fa1ed)
- [👌 Show cleaned up model and parameter
definition](7bdda07)
- [♻️ Converted 4TT to project
API](89ac3a0)
- [♻️ Moved original data dPSI files from data subfolder to
measured_data](85ce095)
- [🧹 Ignore data folders in general since they get populated by
import_data](953dfa5)
- [♻️ Converted dPSI to project
API](73816e0)
- [🧹 Make use of improved project
API](b434331)
- [🧹 Cleaned up rc model and
parameters](079057b)
- [🧹 Cleaned up target_rcg_gcrcg_rcgcr_refine model and
parameters](621113c)
- [🧹 Cleaned up 4TT models and
parameters](f93712f)
- [🧹 Cleaned up dPSI
model](f0deea3)
- [🧹 Cleaned up rc
notebook](3ad4b6c)
- [🔧 Ignore pdfs folder when running
pytest](2a08eee)

---------

Co-authored-by: Ivo van Stokkum <i.h.m.van.stokkum@vu.nl>

.gitignore

@@ -131,6 +131,9 @@ dmypy.json
 # vscode config
 .vscode
 
+# project data folder populated by data_import
+data/
+
 # result folders
 20*/
 results/
@@ -141,3 +144,6 @@ guide/
 
 # Generated PDFs and tex source
 pdfs
+
+# project files
+*.gta

4TT/models/model_refined6osc.yml → 4TT/models/refined6osc.yml

@@ -1,5 +1,3 @@
-# type: doas
-
 initial_concentration:
   j1:
     compartments: [S2, S1, T1, S2rel, T1hot]
@@ -34,9 +32,6 @@ megacomplex:
   decay:
     type: decay
     k_matrix: [k1]
-  #  baseline:
-  #    type: baseline
-  #    dimension: time
   artifact:
     type: coherent-artifact
     order: 3
@@ -52,7 +47,7 @@ irf:
     model_dispersion_with_wavenumber: true
 
 dataset:
-  4TT:
+  corr4TT:
     initial_concentration: j1
     megacomplex: [doas, decay, artifact]
     irf: irf1

4TT/models/model_sequential.yml → 4TT/models/sequential.yml

@@ -1,19 +1,12 @@
-# type: doas
-
 initial_concentration:
   j1:
-    # compartments: [S2, S1, T1, S2rel, T1hot]
-    # parameters: [j.1, j.0, j.0, j.0, j.0]
     compartments: [S2, S1, T1, T1hot]
     parameters: [j.1, j.0, j.0, j.0]
 
 k_matrix:
   k1:
     matrix:
-      # "(S2rel, S2)": kinetic.to_S2rel_from_S2
       "(S1, S2)": kinetic.to_S1_from_S2
-      # "(S1, S2rel)": kinetic.to_S1_from_S2rel
-      # "(T1hot, S2rel)": kinetic.to_T1hot_from_S2rel
       "(T1hot, S1)": kinetic.to_T1hot_from_S1
       "(T1, T1hot)": kinetic.to_T1_from_T1hot
       "(T1, T1)": kinetic.from_T1
@@ -27,9 +20,6 @@ megacomplex:
   decay:
     type: decay
     k_matrix: [k1]
-  #  baseline:
-  #    type: baseline
-  #    dimension: time
   artifact:
     type: coherent-artifact
     order: 3
@@ -45,7 +35,6 @@ irf:
     model_dispersion_with_wavenumber: true
 
 dataset:
-  # dataset1:
   4TT:
     initial_concentration: j1
     megacomplex: [doas, decay, artifact]

4TT/models/model_sequential5osc.yml → 4TT/models/sequential5osc.yml

@@ -1,19 +1,12 @@
-# type: doas
-
 initial_concentration:
   j1:
-    # compartments: [S2, S1, T1, S2rel, T1hot]
-    # parameters: [j.1, j.0, j.0, j.0, j.0]
     compartments: [S2, S1, T1, T1hot]
     parameters: [j.1, j.0, j.0, j.0]
 
 k_matrix:
   k1:
     matrix:
-      # "(S2rel, S2)": kinetic.to_S2rel_from_S2
       "(S1, S2)": kinetic.to_S1_from_S2
-      # "(S1, S2rel)": kinetic.to_S1_from_S2rel
-      # "(T1hot, S2rel)": kinetic.to_T1hot_from_S2rel
       "(T1hot, S1)": kinetic.to_T1hot_from_S1
       "(T1, T1hot)": kinetic.to_T1_from_T1hot
       "(T1, T1)": kinetic.from_T1
@@ -27,9 +20,6 @@ megacomplex:
   decay:
     type: decay
     k_matrix: [k1]
-  #  baseline:
-  #    type: baseline
-  #    dimension: time
   artifact:
     type: coherent-artifact
     order: 3

4TT/models/model_sequential6osc.yml → 4TT/models/sequential6osc.yml

@@ -1,19 +1,12 @@
-# type: doas
-
 initial_concentration:
   j1:
-    # compartments: [S2, S1, T1, S2rel, T1hot]
-    # parameters: [j.1, j.0, j.0, j.0, j.0]
     compartments: [S2, S1, T1, T1hot]
     parameters: [j.1, j.0, j.0, j.0]
 
 k_matrix:
   k1:
     matrix:
-      # "(S2rel, S2)": kinetic.to_S2rel_from_S2
       "(S1, S2)": kinetic.to_S1_from_S2
-      # "(S1, S2rel)": kinetic.to_S1_from_S2rel
-      # "(T1hot, S2rel)": kinetic.to_T1hot_from_S2rel
       "(T1hot, S1)": kinetic.to_T1hot_from_S1
       "(T1, T1hot)": kinetic.to_T1_from_T1hot
       "(T1, T1)": kinetic.from_T1
@@ -36,9 +29,6 @@ megacomplex:
   decay:
     type: decay
     k_matrix: [k1]
-  #  baseline:
-  #    type: baseline
-  #    dimension: time
   artifact:
     type: coherent-artifact
     order: 3
@@ -54,8 +44,7 @@ irf:
     model_dispersion_with_wavenumber: true
 
 dataset:
-  # dataset1:
-  4TT:
+  corr4TT:
     initial_concentration: j1
     megacomplex: [doas, decay, artifact]
     irf: irf1

4TT/models/model.yml → 4TT/models/sequential6osc_S2rel.yml

@@ -1,5 +1,3 @@
-# type: doas
-
 initial_concentration:
   j1:
     compartments: [S2, S1, T1, S2rel, T1hot]
@@ -25,9 +23,6 @@ megacomplex:
   decay:
     type: decay
     k_matrix: [k1]
-  #  baseline:
-  #    type: baseline
-  #    dimension: time
   artifact:
     type: coherent-artifact
     order: 3

4TT/models/parameters_sequential.yml → 4TT/parameters/sequential.yml

@@ -1,8 +1,5 @@
 osc:
   freq: [752.314148, 495.196503, 206.952820, 767.406006, { vary: True }]
-  # rates: [
-  #  3.04113483,    11.2777481,    8.30780029,   -9.46621990,  {vary: True}]
-  # 3.04113483,    11.2777481,    8.3078009,   {vary: True}]
   rates:
     - ["1", 3.04113483, { vary: True }]
     - ["2", 11.2777481, { vary: True }]
@@ -14,10 +11,7 @@ j:
   - ["0", 0.0, { non-negative: False, vary: False }]
 
 kinetic:
-  # - ['to_S2rel_from_S2',6.58372021, {non-negative: True, vary: False}]
   - ["to_S1_from_S2", 8.39700508, { non-negative: True, vary: True }]
-  # - ['to_S1_from_S2rel', 4.36121597, {non-negative: True, vary: False}]
-  # - ['to_T1hot_from_S2rel', 1.6, {non-negative: True, vary: False}]
   - ["to_T1hot_from_S1", 2.24768806, { non-negative: True, vary: True }]
   - ["to_T1_from_T1hot", 0.568519056, { non-negative: True, vary: False }]
   - ["from_T1", 1.00000005E-03, { non-negative: True, vary: False }]

4TT/models/parameters_sequential5osc.yml → 4TT/parameters/sequential5osc.yml

@@ -1,8 +1,5 @@
 osc:
   freq: [752.314148, 495.196503, 206.952820, 767.406006, { vary: True }]
-  # rates: [
-  #  3.04113483,    11.2777481,    8.30780029,   -9.46621990,  {vary: True}]
-  # 3.04113483,    11.2777481,    8.3078009,   {vary: True}]
   rates:
     - ["1", 3.04113483, { vary: True }]
     - ["2", 11.2777481, { vary: True }]
@@ -14,10 +11,7 @@ j:
   - ["0", 0.0, { non-negative: False, vary: False }]
 
 kinetic:
-  # - ['to_S2rel_from_S2',6.58372021, {non-negative: True, vary: False}]
   - ["to_S1_from_S2", 8.39700508, { non-negative: True, vary: True }]
-  # - ['to_S1_from_S2rel', 4.36121597, {non-negative: True, vary: False}]
-  # - ['to_T1hot_from_S2rel', 1.6, {non-negative: True, vary: False}]
   - ["to_T1hot_from_S1", 2.24768806, { non-negative: True, vary: True }]
   - ["to_T1_from_T1hot", 0.568519056, { non-negative: True, vary: True }]
   - ["from_T1", 1.00000005E-03, { non-negative: True, vary: False }]

4TT/models/parameters.yml → 4TT/parameters/sequential6osc_S2rel.yml

@@ -1,8 +1,5 @@
 osc:
   freq: [752.314148, 495.196503, 206.952820, 767.406006, { vary: True }]
-  # rates: [
-  #  3.04113483,    11.2777481,    8.30780029,   -9.46621990,  {vary: True}]
-  # 3.04113483,    11.2777481,    8.3078009,   {vary: True}]
   rates:
     - ["1", 3.04113483, { vary: True }]
     - ["2", 11.2777481, { vary: True }]