data-manipulation-utilities 0.2.4__tar.gz → 0.2.5__tar.gz

{data_manipulation_utilities-0.2.4 → data_manipulation_utilities-0.2.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: data_manipulation_utilities
-Version: 0.2.4
+Version: 0.2.5
 Description-Content-Type: text/markdown
 Requires-Dist: logzero
 Requires-Dist: PyYAML
@@ -26,7 +26,7 @@ These are tools that can be used for different data analysis tasks.
 
 ## Pushing
 
-From the root directory of a version controlled project (i.e. a directory with the `.git` subdirectory) 
+From the root directory of a version controlled project (i.e. a directory with the `.git` subdirectory)
 using a `pyproject.toml` file, run:
 
 ```bash
@@ -36,10 +36,10 @@ publish
 such that:
 
 1. The `pyproject.toml` file is checked and the version of the project is extracted.
-1. If a tag named as the version exists move to the steps below. 
+1. If a tag named as the version exists move to the steps below.
 1. If it does not, make a new tag with the name as the version
 
-Then, for each remote it pushes the tags and the commits. 
+Then, for each remote it pushes the tags and the commits.
 
 *Why?*
 
@@ -137,7 +137,17 @@ pdf   = mod.get_pdf()
 ```
 
 where the model is a sum of three `CrystallBall` PDFs, one with a right tail and two with a left tail.
-The `mu` and `sg` parameters are shared.
+The `mu` and `sg` parameters are shared. The elementary components that can be plugged are:
+
+```
+exp: Exponential
+pol1: Polynomial of degree 1
+pol2: Polynomial of degree 2
+cbr : CrystallBall with right tail
+cbl : CrystallBall with left tail
+gauss : Gaussian 
+dscb : Double sided CrystallBall
+```
 
 ### Printing PDFs
 
@@ -299,7 +309,7 @@ this will:
 - Try fitting at most 10 times
 - After each fit, calculate the goodness of fit (in this case the p-value)
 - Stop when the number of tries has been exhausted or the p-value reached is higher than `0.05`
-- If the fit has not succeeded because of convergence, validity or goodness of fit issues, 
+- If the fit has not succeeded because of convergence, validity or goodness of fit issues,
 randomize the parameters and try again.
 - If the desired goodness of fit has not been achieved, pick the best result.
 - Return the `FitResult` object and set the PDF to the final fit result.
@@ -337,11 +347,11 @@ bkg = zfit.pdf.Exponential(obs=obs, lam=lm)
 nbk = zfit.Parameter('nbk', 1000, 0, 10000)
 ebkg= bkg.create_extended(nbk, name='expo')
 
-# Add them 
+# Add them
 pdf = zfit.pdf.SumPDF([ebkg, esig])
 sam = pdf.create_sampler()
 
-# Plot them 
+# Plot them
 obj   = ZFitPlotter(data=sam, model=pdf)
 d_leg = {'gauss': 'New Gauss'}
 obj.plot(nbins=50, d_leg=d_leg, stacked=True, plot_range=(0, 10), ext_text='Extra text here')
@@ -353,7 +363,7 @@ obj.axs[1].plot([0, 10], [0, 0], linestyle='--', color='black')
 this class supports:
 
 - Handling title, legend, plots size.
-- Adding pulls. 
+- Adding pulls.
 - Stacking and overlaying of PDFs.
 - Blinding.
 
@@ -434,7 +444,7 @@ dataset:
     nan:
         x : 0
         y : 0
-        z : -999 
+        z : -999
 training :
     nfold    : 10
     features : [x, y, z]
@@ -497,7 +507,7 @@ When training on real data, several things might go wrong and the code will try
 will end up in different folds. The tool checks for wether a model is evaluated for an entry that was used for training and raise an exception. Thus, repeated
 entries will be removed before training.
 
-- **NaNs**: Entries with NaNs will break the training with the scikit `GradientBoostClassifier` base class. Thus, we: 
+- **NaNs**: Entries with NaNs will break the training with the scikit `GradientBoostClassifier` base class. Thus, we:
     - Can use the `nan` section shown above to replace `NaN` values with something else
     - For whatever remains we remove the entries from the training.
 
@@ -674,6 +684,9 @@ ptr.run()
 where the config dictionary `cfg_dat` in YAML would look like:
 
 ```yaml
+general:
+    # This will set the figure size
+    size : [20, 10]
 selection:
     #Will do at most 50K random entries. Will only happen if the dataset has more than 50K entries
     max_ran_entries : 50000
@@ -703,6 +716,16 @@ plots:
         yscale     : 'linear'
         labels     : ['x + y', 'Entries']
         normalized : true #This should normalize to the area
+# Some vertical dashed lines are drawn by default
+# If you see them, you can turn them off with this
+style:
+  skip_lines : true
+  # This can pass arguments to legend making function `plt.legend()` in matplotlib
+  legend:
+    # The line below would place the legend outside the figure to avoid ovelaps with the histogram
+    bbox_to_anchor : [1.2, 1]
+stats:
+  nentries : '{:.2e}' # This will add number of entries in legend box
 ```
 
 it's up to the user to build this dictionary and load it.
@@ -724,14 +747,19 @@ The config would look like:
 ```yaml
 saving:
     plt_dir : tests/plotting/2d
+selection:
+  cuts:
+    xlow : x > -1.5
 general:
     size : [20, 10]
 plots_2d:
     # Column x and y
     # Name of column where weights are, null for not weights
     # Name of output plot, e.g. xy_x.png
-    - [x, y, weights, 'xy_w']
-    - [x, y,    null, 'xy_r']
+    # Book signaling to use log scale for z axis
+    - [x, y, weights, 'xy_w', false]
+    - [x, y,    null, 'xy_r', false]
+    - [x, y,    null, 'xy_l',  true]
 axes:
     x :
         binning : [-5.0, 8.0, 40]
@@ -823,7 +851,7 @@ Directory/Treename
     B_ENDVERTEX_CHI2DOF           Double_t
 ```
 
-## Comparing ROOT files 
+## Comparing ROOT files
 
 Given two ROOT files the command below:
 
@@ -885,7 +913,7 @@ last_file = get_latest_file(dir_path = file_dir, wc='name_*.txt')
 # of directories in `dir_path`, e.g.:
 
 oversion=get_last_version(dir_path=dir_path, version_only=True)  # This will return only the version, e.g. v3.2
-oversion=get_last_version(dir_path=dir_path, version_only=False) # This will return full path, e.g. /a/b/c/v3.2 
+oversion=get_last_version(dir_path=dir_path, version_only=False) # This will return full path, e.g. /a/b/c/v3.2
 ```
 
 The function above should work for numeric (e.g. `v1.2`) and non-numeric (e.g. `va`, `vb`) versions.

{data_manipulation_utilities-0.2.4 → data_manipulation_utilities-0.2.5}/README.md

@@ -6,7 +6,7 @@ These are tools that can be used for different data analysis tasks.
 
 ## Pushing
 
-From the root directory of a version controlled project (i.e. a directory with the `.git` subdirectory) 
+From the root directory of a version controlled project (i.e. a directory with the `.git` subdirectory)
 using a `pyproject.toml` file, run:
 
 ```bash
@@ -16,10 +16,10 @@ publish
 such that:
 
 1. The `pyproject.toml` file is checked and the version of the project is extracted.
-1. If a tag named as the version exists move to the steps below. 
+1. If a tag named as the version exists move to the steps below.
 1. If it does not, make a new tag with the name as the version
 
-Then, for each remote it pushes the tags and the commits. 
+Then, for each remote it pushes the tags and the commits.
 
 *Why?*
 
@@ -117,7 +117,17 @@ pdf   = mod.get_pdf()
 ```
 
 where the model is a sum of three `CrystallBall` PDFs, one with a right tail and two with a left tail.
-The `mu` and `sg` parameters are shared.
+The `mu` and `sg` parameters are shared. The elementary components that can be plugged are:
+
+```
+exp: Exponential
+pol1: Polynomial of degree 1
+pol2: Polynomial of degree 2
+cbr : CrystallBall with right tail
+cbl : CrystallBall with left tail
+gauss : Gaussian 
+dscb : Double sided CrystallBall
+```
 
 ### Printing PDFs
 
@@ -279,7 +289,7 @@ this will:
 - Try fitting at most 10 times
 - After each fit, calculate the goodness of fit (in this case the p-value)
 - Stop when the number of tries has been exhausted or the p-value reached is higher than `0.05`
-- If the fit has not succeeded because of convergence, validity or goodness of fit issues, 
+- If the fit has not succeeded because of convergence, validity or goodness of fit issues,
 randomize the parameters and try again.
 - If the desired goodness of fit has not been achieved, pick the best result.
 - Return the `FitResult` object and set the PDF to the final fit result.
@@ -317,11 +327,11 @@ bkg = zfit.pdf.Exponential(obs=obs, lam=lm)
 nbk = zfit.Parameter('nbk', 1000, 0, 10000)
 ebkg= bkg.create_extended(nbk, name='expo')
 
-# Add them 
+# Add them
 pdf = zfit.pdf.SumPDF([ebkg, esig])
 sam = pdf.create_sampler()
 
-# Plot them 
+# Plot them
 obj   = ZFitPlotter(data=sam, model=pdf)
 d_leg = {'gauss': 'New Gauss'}
 obj.plot(nbins=50, d_leg=d_leg, stacked=True, plot_range=(0, 10), ext_text='Extra text here')
@@ -333,7 +343,7 @@ obj.axs[1].plot([0, 10], [0, 0], linestyle='--', color='black')
 this class supports:
 
 - Handling title, legend, plots size.
-- Adding pulls. 
+- Adding pulls.
 - Stacking and overlaying of PDFs.
 - Blinding.
 
@@ -414,7 +424,7 @@ dataset:
     nan:
         x : 0
         y : 0
-        z : -999 
+        z : -999
 training :
     nfold    : 10
     features : [x, y, z]
@@ -477,7 +487,7 @@ When training on real data, several things might go wrong and the code will try
 will end up in different folds. The tool checks for wether a model is evaluated for an entry that was used for training and raise an exception. Thus, repeated
 entries will be removed before training.
 
-- **NaNs**: Entries with NaNs will break the training with the scikit `GradientBoostClassifier` base class. Thus, we: 
+- **NaNs**: Entries with NaNs will break the training with the scikit `GradientBoostClassifier` base class. Thus, we:
     - Can use the `nan` section shown above to replace `NaN` values with something else
     - For whatever remains we remove the entries from the training.
 
@@ -654,6 +664,9 @@ ptr.run()
 where the config dictionary `cfg_dat` in YAML would look like:
 
 ```yaml
+general:
+    # This will set the figure size
+    size : [20, 10]
 selection:
     #Will do at most 50K random entries. Will only happen if the dataset has more than 50K entries
     max_ran_entries : 50000
@@ -683,6 +696,16 @@ plots:
         yscale     : 'linear'
         labels     : ['x + y', 'Entries']
         normalized : true #This should normalize to the area
+# Some vertical dashed lines are drawn by default
+# If you see them, you can turn them off with this
+style:
+  skip_lines : true
+  # This can pass arguments to legend making function `plt.legend()` in matplotlib
+  legend:
+    # The line below would place the legend outside the figure to avoid ovelaps with the histogram
+    bbox_to_anchor : [1.2, 1]
+stats:
+  nentries : '{:.2e}' # This will add number of entries in legend box
 ```
 
 it's up to the user to build this dictionary and load it.
@@ -704,14 +727,19 @@ The config would look like:
 ```yaml
 saving:
     plt_dir : tests/plotting/2d
+selection:
+  cuts:
+    xlow : x > -1.5
 general:
     size : [20, 10]
 plots_2d:
     # Column x and y
     # Name of column where weights are, null for not weights
     # Name of output plot, e.g. xy_x.png
-    - [x, y, weights, 'xy_w']
-    - [x, y,    null, 'xy_r']
+    # Book signaling to use log scale for z axis
+    - [x, y, weights, 'xy_w', false]
+    - [x, y,    null, 'xy_r', false]
+    - [x, y,    null, 'xy_l',  true]
 axes:
     x :
         binning : [-5.0, 8.0, 40]
@@ -803,7 +831,7 @@ Directory/Treename
     B_ENDVERTEX_CHI2DOF           Double_t
 ```
 
-## Comparing ROOT files 
+## Comparing ROOT files
 
 Given two ROOT files the command below:
 
@@ -865,7 +893,7 @@ last_file = get_latest_file(dir_path = file_dir, wc='name_*.txt')
 # of directories in `dir_path`, e.g.:
 
 oversion=get_last_version(dir_path=dir_path, version_only=True)  # This will return only the version, e.g. v3.2
-oversion=get_last_version(dir_path=dir_path, version_only=False) # This will return full path, e.g. /a/b/c/v3.2 
+oversion=get_last_version(dir_path=dir_path, version_only=False) # This will return full path, e.g. /a/b/c/v3.2
 ```
 
 The function above should work for numeric (e.g. `v1.2`) and non-numeric (e.g. `va`, `vb`) versions.

{data_manipulation_utilities-0.2.4 → data_manipulation_utilities-0.2.5}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name        = 'data_manipulation_utilities'
-version     = '0.2.4'
+version     = '0.2.5'
 readme      = 'README.md'
 dependencies= [
 'logzero',

{data_manipulation_utilities-0.2.4 → data_manipulation_utilities-0.2.5}/src/data_manipulation_utilities.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: data_manipulation_utilities
-Version: 0.2.4
+Version: 0.2.5
 Description-Content-Type: text/markdown
 Requires-Dist: logzero
 Requires-Dist: PyYAML
@@ -26,7 +26,7 @@ These are tools that can be used for different data analysis tasks.
 
 ## Pushing
 
-From the root directory of a version controlled project (i.e. a directory with the `.git` subdirectory) 
+From the root directory of a version controlled project (i.e. a directory with the `.git` subdirectory)
 using a `pyproject.toml` file, run:
 
 ```bash
@@ -36,10 +36,10 @@ publish
 such that:
 
 1. The `pyproject.toml` file is checked and the version of the project is extracted.
-1. If a tag named as the version exists move to the steps below. 
+1. If a tag named as the version exists move to the steps below.
 1. If it does not, make a new tag with the name as the version
 
-Then, for each remote it pushes the tags and the commits. 
+Then, for each remote it pushes the tags and the commits.
 
 *Why?*
 
@@ -137,7 +137,17 @@ pdf   = mod.get_pdf()
 ```
 
 where the model is a sum of three `CrystallBall` PDFs, one with a right tail and two with a left tail.
-The `mu` and `sg` parameters are shared.
+The `mu` and `sg` parameters are shared. The elementary components that can be plugged are:
+
+```
+exp: Exponential
+pol1: Polynomial of degree 1
+pol2: Polynomial of degree 2
+cbr : CrystallBall with right tail
+cbl : CrystallBall with left tail
+gauss : Gaussian 
+dscb : Double sided CrystallBall
+```
 
 ### Printing PDFs
 
@@ -299,7 +309,7 @@ this will:
 - Try fitting at most 10 times
 - After each fit, calculate the goodness of fit (in this case the p-value)
 - Stop when the number of tries has been exhausted or the p-value reached is higher than `0.05`
-- If the fit has not succeeded because of convergence, validity or goodness of fit issues, 
+- If the fit has not succeeded because of convergence, validity or goodness of fit issues,
 randomize the parameters and try again.
 - If the desired goodness of fit has not been achieved, pick the best result.
 - Return the `FitResult` object and set the PDF to the final fit result.
@@ -337,11 +347,11 @@ bkg = zfit.pdf.Exponential(obs=obs, lam=lm)
 nbk = zfit.Parameter('nbk', 1000, 0, 10000)
 ebkg= bkg.create_extended(nbk, name='expo')
 
-# Add them 
+# Add them
 pdf = zfit.pdf.SumPDF([ebkg, esig])
 sam = pdf.create_sampler()
 
-# Plot them 
+# Plot them
 obj   = ZFitPlotter(data=sam, model=pdf)
 d_leg = {'gauss': 'New Gauss'}
 obj.plot(nbins=50, d_leg=d_leg, stacked=True, plot_range=(0, 10), ext_text='Extra text here')
@@ -353,7 +363,7 @@ obj.axs[1].plot([0, 10], [0, 0], linestyle='--', color='black')
 this class supports:
 
 - Handling title, legend, plots size.
-- Adding pulls. 
+- Adding pulls.
 - Stacking and overlaying of PDFs.
 - Blinding.
 
@@ -434,7 +444,7 @@ dataset:
     nan:
         x : 0
         y : 0
-        z : -999 
+        z : -999
 training :
     nfold    : 10
     features : [x, y, z]
@@ -497,7 +507,7 @@ When training on real data, several things might go wrong and the code will try
 will end up in different folds. The tool checks for wether a model is evaluated for an entry that was used for training and raise an exception. Thus, repeated
 entries will be removed before training.
 
-- **NaNs**: Entries with NaNs will break the training with the scikit `GradientBoostClassifier` base class. Thus, we: 
+- **NaNs**: Entries with NaNs will break the training with the scikit `GradientBoostClassifier` base class. Thus, we:
     - Can use the `nan` section shown above to replace `NaN` values with something else
     - For whatever remains we remove the entries from the training.
 
@@ -674,6 +684,9 @@ ptr.run()
 where the config dictionary `cfg_dat` in YAML would look like:
 
 ```yaml
+general:
+    # This will set the figure size
+    size : [20, 10]
 selection:
     #Will do at most 50K random entries. Will only happen if the dataset has more than 50K entries
     max_ran_entries : 50000
@@ -703,6 +716,16 @@ plots:
         yscale     : 'linear'
         labels     : ['x + y', 'Entries']
         normalized : true #This should normalize to the area
+# Some vertical dashed lines are drawn by default
+# If you see them, you can turn them off with this
+style:
+  skip_lines : true
+  # This can pass arguments to legend making function `plt.legend()` in matplotlib
+  legend:
+    # The line below would place the legend outside the figure to avoid ovelaps with the histogram
+    bbox_to_anchor : [1.2, 1]
+stats:
+  nentries : '{:.2e}' # This will add number of entries in legend box
 ```
 
 it's up to the user to build this dictionary and load it.
@@ -724,14 +747,19 @@ The config would look like:
 ```yaml
 saving:
     plt_dir : tests/plotting/2d
+selection:
+  cuts:
+    xlow : x > -1.5
 general:
     size : [20, 10]
 plots_2d:
     # Column x and y
     # Name of column where weights are, null for not weights
     # Name of output plot, e.g. xy_x.png
-    - [x, y, weights, 'xy_w']
-    - [x, y,    null, 'xy_r']
+    # Book signaling to use log scale for z axis
+    - [x, y, weights, 'xy_w', false]
+    - [x, y,    null, 'xy_r', false]
+    - [x, y,    null, 'xy_l',  true]
 axes:
     x :
         binning : [-5.0, 8.0, 40]
@@ -823,7 +851,7 @@ Directory/Treename
     B_ENDVERTEX_CHI2DOF           Double_t
 ```
 
-## Comparing ROOT files 
+## Comparing ROOT files
 
 Given two ROOT files the command below:
 
@@ -885,7 +913,7 @@ last_file = get_latest_file(dir_path = file_dir, wc='name_*.txt')
 # of directories in `dir_path`, e.g.:
 
 oversion=get_last_version(dir_path=dir_path, version_only=True)  # This will return only the version, e.g. v3.2
-oversion=get_last_version(dir_path=dir_path, version_only=False) # This will return full path, e.g. /a/b/c/v3.2 
+oversion=get_last_version(dir_path=dir_path, version_only=False) # This will return full path, e.g. /a/b/c/v3.2
 ```
 
 The function above should work for numeric (e.g. `v1.2`) and non-numeric (e.g. `va`, `vb`) versions.

{data_manipulation_utilities-0.2.4 → data_manipulation_utilities-0.2.5}/src/data_manipulation_utilities.egg-info/SOURCES.txt

@@ -38,10 +38,12 @@ src/dmu_data/ml/tests/train_mva.yaml
 src/dmu_data/plotting/tests/2d.yaml
 src/dmu_data/plotting/tests/fig_size.yaml
 src/dmu_data/plotting/tests/high_stat.yaml
+src/dmu_data/plotting/tests/legend.yaml
 src/dmu_data/plotting/tests/name.yaml
 src/dmu_data/plotting/tests/no_bounds.yaml
 src/dmu_data/plotting/tests/normalized.yaml
 src/dmu_data/plotting/tests/simple.yaml
+src/dmu_data/plotting/tests/stats.yaml
 src/dmu_data/plotting/tests/title.yaml
 src/dmu_data/plotting/tests/weights.yaml
 src/dmu_data/text/transform.toml

{data_manipulation_utilities-0.2.4 → data_manipulation_utilities-0.2.5}/src/dmu/ml/cv_classifier.py

@@ -1,15 +1,15 @@
 '''
 Module holding cv_classifier class
 '''
-
+import os
 from typing                  import Union
 from sklearn.ensemble        import GradientBoostingClassifier
 
+import yaml
 from dmu.logging.log_store import LogStore
 import dmu.ml.utilities    as ut
 
 log = LogStore.add_logger('dmu:ml:CVClassifier')
-
 # ---------------------------------------
 class CVSameData(Exception):
     '''
@@ -61,6 +61,20 @@ class CVClassifier(GradientBoostingClassifier):
 
         return self._cfg
     # ----------------------------------
+    def save_cfg(self, path : str):
+        '''
+        Will save configuration used to train this classifier to YAML
+
+        path: Path to YAML file
+        '''
+        dir_name = os.path.dirname(path)
+        os.makedirs(dir_name, exist_ok=True)
+
+        with open(path, 'w', encoding='utf-8') as ofile:
+            yaml.safe_dump(self._cfg, ofile, indent=2)
+
+        log.info(f'Saved config to: {path}')
+    # ----------------------------------
     def __str__(self):
         nhash = len(self._s_hash)
 

{data_manipulation_utilities-0.2.4 → data_manipulation_utilities-0.2.5}/src/dmu/ml/cv_predict.py

@@ -73,11 +73,11 @@ class CVPredict:
             log.debug('Not doing any NaN replacement')
             return df
 
-        log.debug(60 * '-')
+        log.info(60 * '-')
         log.info('Doing NaN replacements')
-        log.debug(60 * '-')
+        log.info(60 * '-')
         for var, val in self._d_nan_rep.items():
-            log.debug(f'{var:<20}{"--->":20}{val:<20.3f}')
+            log.info(f'{var:<20}{"--->":20}{val:<20.3f}')
             df[var] = df[var].fillna(val)
 
         return df
@@ -155,7 +155,7 @@ class CVPredict:
         ndif = len(s_dif_hash)
         ndat = len(s_dat_hash)
         nmod = len(s_mod_hash)
-        log.debug(f'{ndif:<20}{"=":10}{ndat:<20}{"-":10}{nmod:<20}')
+        log.debug(f'{ndif:<10}{"=":5}{ndat:<10}{"-":5}{nmod:<10}')
 
         df_ft_group= df_ft.loc[df_ft.index.isin(s_dif_hash)]
 
@@ -173,7 +173,7 @@ class CVPredict:
             return arr_prb
 
         nentries = len(self._arr_patch)
-        log.warning(f'Patching {nentries} probabilities')
+        log.warning(f'Patching {nentries} probabilities with -1')
         arr_prb[self._arr_patch] = -1
 
         return arr_prb

{data_manipulation_utilities-0.2.4 → data_manipulation_utilities-0.2.5}/src/dmu/ml/train_mva.py

@@ -69,14 +69,20 @@ class TrainMva:
         return df, arr_lab
     # ---------------------------------------------
     def _pre_process_nans(self, df : pnd.DataFrame) -> pnd.DataFrame:
+        if 'dataset' not in self._cfg:
+            return df
+
         if 'nan' not in self._cfg['dataset']:
             log.debug('dataset/nan section not found, not pre-processing NaNs')
             return df
 
         d_name_val = self._cfg['dataset']['nan']
-        for name, val in d_name_val.items():
-            log.debug(f'{val:<20}{"<---":<10}{name:<100}')
-            df[name] = df[name].fillna(val)
+        log.info(60 * '-')
+        log.info('Doing NaN replacements')
+        log.info(60 * '-')
+        for var, val in d_name_val.items():
+            log.info(f'{var:<20}{"--->":20}{val:<20.3f}')
+            df[var] = df[var].fillna(val)
 
         return df
     # ---------------------------------------------
@@ -406,6 +412,9 @@ class TrainMva:
         self._save_hyperparameters_to_tex()
     # ---------------------------------------------
     def _save_nan_conversion(self) -> None:
+        if 'dataset' not in self._cfg:
+            return
+
         if 'nan' not in self._cfg['dataset']:
             log.debug('NaN section not found, not saving it')
             return
@@ -434,13 +443,18 @@ class TrainMva:
         os.makedirs(val_dir, exist_ok=True)
         put.df_to_tex(df, f'{val_dir}/hyperparameters.tex')
     # ---------------------------------------------
-    def run(self):
+    def run(self, skip_fit : bool = False) -> None:
         '''
         Will do the training
+
+        skip_fit: By default false, if True, it will only do the plots of features and save tables
         '''
         self._save_settings_to_tex()
         self._plot_features()
 
+        if skip_fit:
+            return
+
         l_mod = self._get_models()
         for ifold, mod in enumerate(l_mod):
             self._save_model(mod, ifold)

{data_manipulation_utilities-0.2.4 → data_manipulation_utilities-0.2.5}/src/dmu/ml/utilities.py

@@ -16,7 +16,7 @@ log = LogStore.add_logger('dmu:ml:utilities')
 # ---------------------------------------------
 def patch_and_tag(df : pnd.DataFrame, value : float = 0) -> pnd.DataFrame:
     '''
-    Takes panda dataframe, replaces NaNs with value introduced, by default 0
+    Takes pandas dataframe, replaces NaNs with value introduced, by default 0
     Returns array of indices where the replacement happened
     '''
     l_nan = df.index[df.isna().any(axis=1)].tolist()
@@ -25,7 +25,13 @@ def patch_and_tag(df : pnd.DataFrame, value : float = 0) -> pnd.DataFrame:
         log.debug('No NaNs found')
         return df
 
-    log.warning(f'Found {nnan} NaNs, patching them with {value}')
+    log.warning(f'Found {nnan} NaNs')
+
+    df_nan_frq = df.isna().sum()
+    df_nan_frq = df_nan_frq[df_nan_frq > 0]
+    print(df_nan_frq)
+
+    log.warning(f'Attaching array with NaN {nnan} indexes and removing NaNs from dataframe')
 
     df_pa = df.fillna(value)
 
@@ -57,7 +63,7 @@ def _remove_nans(df : pnd.DataFrame) -> pnd.DataFrame:
     log.info('Found columns with NaNs')
     for name in l_na_name:
         nan_count = df[name].isna().sum()
-        log.info(f'{nan_count:<10}{name:<100}')
+        log.info(f'{nan_count:<10}{name}')
 
     ninit = len(df)
     df    = df.dropna()
@@ -75,10 +81,10 @@ def _remove_repeated(df : pnd.DataFrame) -> pnd.DataFrame:
     nfinl = len(s_hash)
 
     if ninit == nfinl:
-        log.debug('No cleaning needed for dataframe')
+        log.debug('No overlap between training and application found')
         return df
 
-    log.warning(f'Repeated entries found, cleaning up: {ninit} -> {nfinl}')
+    log.warning(f'Overlap between training and application found, cleaning up: {ninit} -> {nfinl}')
 
     df['hash_index'] = l_hash
     df               = df.set_index('hash_index', drop=True)

{data_manipulation_utilities-0.2.4 → data_manipulation_utilities-0.2.5}/src/dmu/plotting/plotter.py

@@ -107,7 +107,7 @@ class Plotter:
 
         d_cut = self._d_cfg['selection']['cuts']
 
-        log.info('Applying cuts')
+        log.debug('Applying cuts')
         for name, cut in d_cut.items():
             log.debug(f'{name:<50}{cut:<150}')
             rdf = rdf.Filter(cut, name)
@@ -212,7 +212,11 @@ class Plotter:
 
         var (str) : Name of variable, needed for plot name
         '''
-        plt.legend()
+        d_leg = {}
+        if 'style' in self._d_cfg and 'legend' in self._d_cfg['style']:
+            d_leg = self._d_cfg['style']['legend']
+
+        plt.legend(**d_leg)
 
         plt_dir = self._d_cfg['saving']['plt_dir']
         os.makedirs(plt_dir, exist_ok=True)

{data_manipulation_utilities-0.2.4 → data_manipulation_utilities-0.2.5}/src/dmu/plotting/plotter_1d.py

@@ -77,17 +77,33 @@ class Plotter1D(Plotter):
 
         l_bc_all = []
         for name, arr_val in d_data.items():
+            label        = self._label_from_name(name, arr_val)
             arr_wgt      = d_wgt[name] if d_wgt is not None else numpy.ones_like(arr_val)
             arr_wgt      = self._normalize_weights(arr_wgt, var)
-            hst          = Hist.new.Reg(bins=bins, start=minx, stop=maxx, name='x', label=name).Weight()
+            hst          = Hist.new.Reg(bins=bins, start=minx, stop=maxx, name='x').Weight()
             hst.fill(x=arr_val, weight=arr_wgt)
-            hst.plot(label=name)
+            hst.plot(label=label)
             l_bc_all    += hst.values().tolist()
 
         max_y = max(l_bc_all)
 
         return max_y
     # --------------------------------------------
+    def _label_from_name(self, name : str, arr_val : numpy.ndarray) -> str:
+        if 'stats' not in self._d_cfg:
+            return name
+
+        d_stat = self._d_cfg['stats']
+        if 'nentries' not in d_stat:
+            return name
+
+        form = d_stat['nentries']
+
+        nentries = len(arr_val)
+        nentries = form.format(nentries)
+
+        return f'{name}{nentries}'
+    # --------------------------------------------
     def _normalize_weights(self, arr_wgt : numpy.ndarray, var : str) -> numpy.ndarray:
         cfg_var = self._d_cfg['plots'][var]
         if 'normalized' not in cfg_var:
@@ -104,7 +120,6 @@ class Plotter1D(Plotter):
 
         return arr_wgt
     # --------------------------------------------
-
     def _style_plot(self, var : str, max_y : float) -> None:
         d_cfg  = self._d_cfg['plots'][var]
         yscale = d_cfg['yscale' ] if 'yscale' in d_cfg else 'linear'
@@ -124,12 +139,15 @@ class Plotter1D(Plotter):
         plt.legend()
         plt.title(title)
     # --------------------------------------------
-    def _plot_lines(self, var : str):
+    def _plot_lines(self, var : str) -> None:
         '''
         Will plot vertical lines for some variables
 
         var (str) : name of variable
         '''
+        if 'style' in self._d_cfg and 'skip_lines' in self._d_cfg['style'] and self._d_cfg['style']['skip_lines']:
+            return
+
         if var in ['B_const_mass_M', 'B_M']:
             plt.axvline(x=5280, color='r', label=r'$B^+$'   , linestyle=':')
         elif var == 'Jpsi_M':

{data_manipulation_utilities-0.2.4 → data_manipulation_utilities-0.2.5}/src/dmu/plotting/plotter_2d.py

@@ -10,6 +10,7 @@ import matplotlib.pyplot as plt
 
 from hist                  import Hist
 from ROOT                  import RDataFrame
+from matplotlib.colors     import LogNorm
 from dmu.logging.log_store import LogStore
 from dmu.plotting.plotter  import Plotter
 
@@ -28,11 +29,8 @@ class Plotter2D(Plotter):
         cfg   (dict): Dictionary with configuration, e.g. binning, ranges, etc
         '''
 
-        if not isinstance(cfg, dict):
-            raise ValueError('Config dictionary not passed')
-
-        self._d_cfg : dict       = cfg
-        self._rdf   : RDataFrame = super()._preprocess_rdf(rdf)
+        super().__init__({'single_rdf' : rdf}, cfg)
+        self._rdf : RDataFrame = self._d_rdf['single_rdf']
 
         self._wgt : numpy.ndarray
     # --------------------------------------------
@@ -61,7 +59,7 @@ class Plotter2D(Plotter):
 
         return arr_wgt
     # --------------------------------------------
-    def _plot_vars(self, varx : str, vary : str, wgt_name : str) -> None:
+    def _plot_vars(self, varx : str, vary : str, wgt_name : str, use_log : bool) -> None:
         log.info(f'Plotting {varx} vs {vary} with weights {wgt_name}')
 
         ax_x         = self._get_axis(varx)
@@ -72,7 +70,10 @@ class Plotter2D(Plotter):
         hst   = Hist(ax_x, ax_y)
         hst.fill(arr_x, arr_y, weight=arr_w)
 
-        mplhep.hist2dplot(hst)
+        if use_log:
+            mplhep.hist2dplot(hst, norm=LogNorm())
+        else:
+            mplhep.hist2dplot(hst)
     # --------------------------------------------
     def run(self):
         '''
@@ -80,8 +81,8 @@ class Plotter2D(Plotter):
         '''
 
         fig_size = self._get_fig_size()
-        for [varx, vary, wgt_name, plot_name] in self._d_cfg['plots_2d']:
+        for [varx, vary, wgt_name, plot_name, use_log] in self._d_cfg['plots_2d']:
             plt.figure(plot_name, figsize=fig_size)
-            self._plot_vars(varx, vary, wgt_name)
+            self._plot_vars(varx, vary, wgt_name, use_log)
             self._save_plot(plot_name)
 # --------------------------------------------

{data_manipulation_utilities-0.2.4 → data_manipulation_utilities-0.2.5}/src/dmu/stats/model_factory.py

@@ -1,7 +1,7 @@
 '''
 Module storing ZModel class
 '''
-# pylint: disable=too-many-lines, import-error
+# pylint: disable=too-many-lines, import-error, too-many-positional-arguments, too-many-arguments
 
 from typing import Callable, Union
 
@@ -69,12 +69,18 @@ class ModelFactory:
 
         self._d_par : dict[str,zpar] = {}
     #-----------------------------------------
+    def _fltname_from_name(self, name : str) -> str:
+        if name in ['mu', 'sg']:
+            return f'{name}_flt'
+
+        return name
+    #-----------------------------------------
     def _get_name(self, name : str, suffix : str) -> str:
         for can_be_shared in self._l_can_be_shared:
             if name.startswith(f'{can_be_shared}_') and can_be_shared in self._l_shr:
-                return can_be_shared
+                return self._fltname_from_name(can_be_shared)
 
-        return f'{name}{suffix}'
+        return self._fltname_from_name(f'{name}{suffix}')
     #-----------------------------------------
     def _get_parameter(self,
                        name   : str,
@@ -129,8 +135,8 @@ class ModelFactory:
     def _get_cbl(self, suffix : str = '') -> zpdf:
         mu  = self._get_parameter('mu_cbl', suffix, 5300, 5250, 5350)
         sg  = self._get_parameter('sg_cbl', suffix,   10,    2,  300)
-        al  = self._get_parameter('ac_cbl', suffix,    2,   1.,   4.)
-        nl  = self._get_parameter('nc_cbl', suffix,    1,  0.5,  5.0)
+        al  = self._get_parameter('ac_cbl', suffix,    2,   1.,  14.)
+        nl  = self._get_parameter('nc_cbl', suffix,    1,  0.5,  15.)
 
         pdf = zfit.pdf.CrystalBall(mu, sg, al, nl, self._obs)
 
@@ -151,8 +157,8 @@ class ModelFactory:
         sg  = self._get_parameter('sg_dscb', suffix,   10,    2,   30)
         ar  = self._get_parameter('ar_dscb', suffix,    1,    0,    5)
         al  = self._get_parameter('al_dscb', suffix,    1,    0,    5)
-        nr  = self._get_parameter('nr_dscb', suffix,    2,    1,    5)
-        nl  = self._get_parameter('nl_dscb', suffix,    2,    0,    5)
+        nr  = self._get_parameter('nr_dscb', suffix,    2,    1,   15)
+        nl  = self._get_parameter('nl_dscb', suffix,    2,    0,   15)
 
         pdf = zfit.pdf.DoubleCB(mu, sg, al, nl, ar, nr, self._obs)
 

{data_manipulation_utilities-0.2.4 → data_manipulation_utilities-0.2.5}/src/dmu/testing/utilities.py

@@ -2,6 +2,7 @@
 Module containing utility functions needed by unit tests
 '''
 import os
+import math
 from typing              import Union
 from dataclasses         import dataclass
 from importlib.resources import files
@@ -21,56 +22,64 @@ class Data:
     '''
     Class storing shared data
     '''
-    nentries = 3000
 # -------------------------------
-def _double_data(d_data : dict) -> dict:
-    df_1   = pnd.DataFrame(d_data)
-    df_2   = pnd.DataFrame(d_data)
-
+def _double_data(df_1 : pnd.DataFrame) -> pnd.DataFrame:
+    df_2   = df_1.copy()
     df     = pnd.concat([df_1, df_2], axis=0)
 
-    d_data = { name : df[name].to_numpy() for name in df.columns }
-
-    return d_data
+    return df
 # -------------------------------
-def _add_nans(d_data : dict) -> dict:
-    df_good   = pnd.DataFrame(d_data)
-    df_bad    = pnd.DataFrame(d_data)
-    df_bad[:] = numpy.nan
+def _add_nans(df : pnd.DataFrame, columns : list[str]) -> pnd.DataFrame:
+    size = len(df) * 0.2
+    size = math.floor(size)
+
+    l_col = df.columns.tolist()
+    if columns is None:
+        l_col_index = range(len(l_col))
+    else:
+        l_col_index = [ l_col.index(column) for column in columns ]
 
-    df        = pnd.concat([df_good, df_bad])
-    d_data    = { name : df[name].to_numpy() for name in df.columns }
+    log.debug('Replacing randomly with {size} NaNs')
+    for _ in range(size):
+        irow = numpy.random.randint(0, df.shape[0])      # Random row index
+        icol = numpy.random.choice(l_col_index)      # Random column index
 
-    return d_data
+        df.iat[irow, icol] = numpy.nan
+
+    return df
 # -------------------------------
 def get_rdf(kind : Union[str,None] = None,
             repeated : bool        = False,
-            add_nans : bool        = False):
+            nentries : int         = 3_000,
+            add_nans : list[str]   = None):
     '''
     Return ROOT dataframe with toy data
     '''
+
     d_data = {}
     if   kind == 'sig':
-        d_data['w'] = numpy.random.normal(0, 1, size=Data.nentries)
-        d_data['x'] = numpy.random.normal(0, 1, size=Data.nentries)
-        d_data['y'] = numpy.random.normal(0, 1, size=Data.nentries)
-        d_data['z'] = numpy.random.normal(0, 1, size=Data.nentries)
+        d_data['w'] = numpy.random.normal(0, 1, size=nentries)
+        d_data['x'] = numpy.random.normal(0, 1, size=nentries)
+        d_data['y'] = numpy.random.normal(0, 1, size=nentries)
+        d_data['z'] = numpy.random.normal(0, 1, size=nentries)
     elif kind == 'bkg':
-        d_data['w'] = numpy.random.normal(1, 1, size=Data.nentries)
-        d_data['x'] = numpy.random.normal(1, 1, size=Data.nentries)
-        d_data['y'] = numpy.random.normal(1, 1, size=Data.nentries)
-        d_data['z'] = numpy.random.normal(1, 1, size=Data.nentries)
+        d_data['w'] = numpy.random.normal(1, 1, size=nentries)
+        d_data['x'] = numpy.random.normal(1, 1, size=nentries)
+        d_data['y'] = numpy.random.normal(1, 1, size=nentries)
+        d_data['z'] = numpy.random.normal(1, 1, size=nentries)
     else:
         log.error(f'Invalid kind: {kind}')
         raise ValueError
 
+    df = pnd.DataFrame(d_data)
+
     if repeated:
-        d_data = _double_data(d_data)
+        df = _double_data(df)
 
     if add_nans:
-        d_data = _add_nans(d_data)
+        df = _add_nans(df, columns=add_nans)
 
-    rdf = RDF.FromNumpy(d_data)
+    rdf = RDF.FromPandas(df)
 
     return rdf
 # -------------------------------

{data_manipulation_utilities-0.2.4 → data_manipulation_utilities-0.2.5}/src/dmu_data/ml/tests/train_mva.yaml

@@ -1,6 +1,7 @@
 dataset:
   nan :
-    x : 0
+    x : 1
+    y : 2
 training :
     nfold    : 3
     features : [x, y, z]
@@ -33,10 +34,6 @@ plotting:
         saving:
             plt_dir : '/tmp/dmu/ml/tests/train_mva/features'
         plots:
-          w :
-            binning : [-4, 4, 100]
-            yscale  : 'linear'
-            labels  : ['w', '']
           x :
             binning : [-4, 4, 100]
             yscale  : 'linear'

{data_manipulation_utilities-0.2.4 → data_manipulation_utilities-0.2.5}/src/dmu_data/plotting/tests/2d.yaml

@@ -1,13 +1,17 @@
 saving:
-    plt_dir : tests/plotting/2d_weighted
+    plt_dir : /tmp/dmu/tests/plotting/2d_weighted
+selection:
+  cuts:
+    xlow : x > -1.5
 definitions:
   z : x + y
 general:
     size : [20, 10]
 plots_2d:
-    - [x, y, weights, 'xy_w']
-    - [x, y,    null, 'xy_r']
-    - [x, z,    null, 'xz_r']
+    - [x, y, weights, 'xy_wgt', false]
+    - [x, y,    null, 'xy_raw', false]
+    - [x, z,    null, 'xz_raw', false]
+    - [x, z,    null, 'xz_log',  true]
 axes:
     x :
         binning : [-3.0, 3.0, 40]

data_manipulation_utilities-0.2.5/src/dmu_data/plotting/tests/legend.yaml

@@ -0,0 +1,12 @@
+saving:
+    plt_dir : tests/plotting/legend
+general:
+    size : [20, 10]
+plots:
+    x : 
+        binning : [-5.0, 8.0, 40]
+    y : 
+        binning : [-5.0, 8.0, 40]
+style:
+  legend:
+    bbox_to_anchor : [1.2, 1]

data_manipulation_utilities-0.2.5/src/dmu_data/plotting/tests/stats.yaml

@@ -0,0 +1,9 @@
+saving:
+    plt_dir : tests/plotting/stats
+plots:
+    x : 
+        binning : [-5.0, 8.0, 40]
+    y : 
+        binning : [-5.0, 8.0, 40]
+stats:
+  nentries : '{:.2e}'