tadamz 0.13.0a1__tar.gz

tadamz-0.13.0a1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) [2023] [Patrick Kiefer]
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

tadamz-0.13.0a1/MANIFEST.in

@@ -0,0 +1,7 @@
+recursive-include src/tadamz *.table
+recursive-include src/tadamz *.xlsx
+recursive-include src/tadamz *.txt
+recursive-include src/tadamz *.onnx
+recursive-inclöude docs *.md
+
+recursive-exclude * __pycache__

tadamz-0.13.0a1/PKG-INFO

@@ -0,0 +1,123 @@
+Metadata-Version: 2.4
+Name: tadamz
+Version: 0.13.0a1
+Summary: package for targeted LC-MS(/MS) data analysis
+Author: Patrick
+Author-email: pkiefer@ethz.ch
+License: MIT License
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: End Users/Desktop
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pyyaml
+Requires-Dist: uncertainties
+Requires-Dist: skl2onnx==1.16.0
+Requires-Dist: onnx==1.16.1
+Requires-Dist: onnxruntime==1.16.3
+Requires-Dist: pybaselines==1.1.0
+Requires-Dist: emzed>=3.0.0a16
+Dynamic: license-file
+
+# tadamz
+
+
+
+## Getting started
+
+To make it easy for you to get started with GitLab, here's a list of recommended next steps.
+
+Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
+
+## Add your files
+
+- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
+- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
+
+```
+cd existing_repo
+git remote add origin https://gitlab.com/emzed3_extensions/targeted.git
+git branch -M main
+git push -uf origin main
+```
+
+## Integrate with your tools
+
+- [ ] [Set up project integrations](https://gitlab.com/emzed3_extensions/targeted/-/settings/integrations)
+
+## Collaborate with your team
+
+- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
+- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
+- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
+- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
+- [ ] [Automatically merge when pipeline succeeds](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
+
+## Test and Deploy
+
+Use the built-in continuous integration in GitLab.
+
+- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
+- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing(SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
+- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
+- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
+- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
+
+***
+
+# Editing this README
+
+When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thank you to [makeareadme.com](https://www.makeareadme.com/) for this template.
+
+## Suggestions for a good README
+Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
+
+## Name
+Choose a self-explaining name for your project.
+
+## Description
+Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
+
+## Badges
+On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
+
+## Visuals
+Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
+
+## Installation
+The package tadamz can be installed using pip, either within a separate venv or from the emzed-spyder IPython console:
+~~~
+pip install https://gitlab.com/emzed3_extensions/targeted.git
+~~~~
+emzed, emzed-webgui, and pyaml will be installed automatically as a dependencies if necessary.
+
+## Usage
+Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
+
+## Support
+Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
+
+## Roadmap
+If you have ideas for releases in the future, it is a good idea to list them in the README.
+
+## Contributing
+State if you are open to contributions and what your requirements are for accepting them.
+
+For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
+
+You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
+
+## Authors and acknowledgment
+Show your appreciation to those who have contributed to the project.
+
+## License
+For open source projects, say how it is licensed.
+
+## Project status
+If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.

tadamz-0.13.0a1/README.md

@@ -0,0 +1,96 @@
+# tadamz
+
+
+
+## Getting started
+
+To make it easy for you to get started with GitLab, here's a list of recommended next steps.
+
+Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
+
+## Add your files
+
+- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
+- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
+
+```
+cd existing_repo
+git remote add origin https://gitlab.com/emzed3_extensions/targeted.git
+git branch -M main
+git push -uf origin main
+```
+
+## Integrate with your tools
+
+- [ ] [Set up project integrations](https://gitlab.com/emzed3_extensions/targeted/-/settings/integrations)
+
+## Collaborate with your team
+
+- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
+- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
+- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
+- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
+- [ ] [Automatically merge when pipeline succeeds](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
+
+## Test and Deploy
+
+Use the built-in continuous integration in GitLab.
+
+- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
+- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing(SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
+- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
+- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
+- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
+
+***
+
+# Editing this README
+
+When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thank you to [makeareadme.com](https://www.makeareadme.com/) for this template.
+
+## Suggestions for a good README
+Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
+
+## Name
+Choose a self-explaining name for your project.
+
+## Description
+Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
+
+## Badges
+On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
+
+## Visuals
+Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
+
+## Installation
+The package tadamz can be installed using pip, either within a separate venv or from the emzed-spyder IPython console:
+~~~
+pip install https://gitlab.com/emzed3_extensions/targeted.git
+~~~~
+emzed, emzed-webgui, and pyaml will be installed automatically as a dependencies if necessary.
+
+## Usage
+Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
+
+## Support
+Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
+
+## Roadmap
+If you have ideas for releases in the future, it is a good idea to list them in the README.
+
+## Contributing
+State if you are open to contributions and what your requirements are for accepting them.
+
+For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
+
+You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
+
+## Authors and acknowledgment
+Show your appreciation to those who have contributed to the project.
+
+## License
+For open source projects, say how it is licensed.
+
+## Project status
+If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.

tadamz-0.13.0a1/pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools >= 40.6.0", "wheel"]
+build-backend = "setuptools.build_meta"

tadamz-0.13.0a1/setup.cfg

@@ -0,0 +1,45 @@
+[metadata]
+name = tadamz
+version = attr: tadamz.__version__
+license = MIT License
+description = package for targeted LC-MS(/MS) data analysis
+long_description = file: README.md
+long_description_content_type = text/markdown
+author = Patrick
+author_email = pkiefer@ethz.ch
+classifiers = 
+	Intended Audience :: Science/Research
+	Intended Audience :: End Users/Desktop
+	License :: OSI Approved :: MIT License
+	Natural Language :: English
+	Programming Language :: Python :: 3
+	Programming Language :: Python :: 3.9
+	Programming Language :: Python :: 3.10
+	Operating System :: OS Independent
+
+[options]
+install_requires = 
+	pyyaml
+	uncertainties
+	skl2onnx==1.16.0
+	onnx==1.16.1
+	onnxruntime==1.16.3
+	pybaselines==1.1.0
+	emzed>=3.0.0a16
+include_package_data = True
+packages = find:
+package_dir = 
+	=src
+zip_safe = False
+python_requires = >=3.10
+
+[options.packages.find]
+where = src
+
+[options.package_data]
+* = *.txt, *.xlsx,  *.table , *.md, *.onnx
+
+[egg_info]
+tag_build = 
+tag_date = 0
+

tadamz-0.13.0a1/src/tadamz/__init__.py

@@ -0,0 +1,28 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Jul  3 15:56:21 2023
+
+@author: pkiefer
+"""
+__author__ = "Patrick Kiefer"
+__email__ = "pkiefer@ethz.ch"
+__credits__ = "ETH Zurich, Institute of Microbiology"
+
+__version__ = "0.13.0a1"
+
+# from . import score_peaks_quality
+# from . import extract_peaks
+from .in_out import load_config
+
+# from .calibration.basic_calibration_functions import CalibrationModel
+from . import workflow
+
+# sfrom . calibration import basic_calibration_functions
+# from . import normalize_peaks
+# from . import peaks_table
+# from . import processing_steps
+# from . import quantify
+# from . import utils
+# from . import workflow
+from .workflow import run_workflow, postprocess_result_table, run_calibration
+from .create_random_forest_peak_classifier import generate_peak_classifier

tadamz-0.13.0a1/src/tadamz/adapt_retention_time.py

@@ -0,0 +1,329 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Feb 21 12:56:10 2023
+
+@author: pkiefer
+Concept
+There are 2 approaches 
+1) via fit (in that case the alignment peaks_table originates from a measurement)
+2) from internal standard: The simplest approach: we select most important 
+peak based on internal standard: Problems of mass isomers;
+-> solutions 
+The risk in case of several in
+
+"""
+import numpy as np
+from emzed import RtType, Table
+from emzed.quantification import integrate_chromatograms
+
+
+######################################################
+# Local adaptation
+
+
+from scipy.signal import savgol_filter
+
+
+def local_adjust(t, min_fwhm=2.0, integration_algorithm="linear"):
+    _determine_shift(t)
+    _set_windows(t, min_fwhm, "rt_chromatogram")
+    integrate_chromatograms(t, integration_algorithm, in_place=True)
+    t.add_or_replace_column(
+        "rt_chromatogram",
+        t.apply(determine_rt, t.model_chromatogram, t.rt_chromatogram),
+        RtType,
+    )
+
+
+def _determine_shift(t):
+    t.add_column("lboundary", t.rtmin_chromatogram - t.rt_chromatogram, RtType)
+    t.add_column("rboundary", t.rtmax_chromatogram - t.rt_chromatogram, RtType)
+    _update_spectral_distance(t)
+    t.replace_column(
+        "rtmin_chromatogram",
+        (t.rt_max_shift > 0).then_else(
+            t.rt_chromatogram - t.rt_max_shift, t.rt_chromatogram - t.min_tol
+        ),
+        RtType,
+    )
+    t.replace_column(
+        "rtmax_chromatogram",
+        (t.rt_max_shift > 0).then_else(
+            t.rt_chromatogram + t.rt_max_shift, t.rt_chromatogram + t.min_tol
+        ),
+        RtType,
+    )
+    integrate_chromatograms(t, "linear", in_place=True)
+    t.add_column(
+        "temp", t.apply(determine_rt, t.model_chromatogram, t.rt_chromatogram), RtType
+    )
+    t.replace_column("temp", t.temp.if_not_none_else(t.rt_chromatogram), RtType)
+    t.replace_column("rtmin_chromatogram", t.lboundary + t.temp, RtType)
+    t.replace_column("rtmax_chromatogram", t.rboundary + t.temp, RtType)
+    integrate_chromatograms(t, "linear", in_place=True)
+    t.drop_columns("lboundary", "rboundary", "temp", "min_tol")
+
+
+def _update_spectral_distance(t):
+    t.add_column(
+        "min_tol",
+        t.apply(
+            _max_delta_spec,
+            t.chromatogram,
+            t.rtmin_chromatogram,
+            t.rtmax_chromatogram,
+            t.rt_max_shift,
+            ignore_nones=False,
+        ),
+        RtType,
+    )
+
+
+def _max_delta_spec(*kwargs):
+    epsilon = 1e-2  # value to increase numerical stability but with no significant influence on
+    # rt shift
+    if not _check_params(kwargs):
+        return epsilon
+    chrom, rtmin, rtmax, rttol = kwargs
+    rts = chrom.rts
+    peak_range = rts[(rts >= rtmin - rttol) & (rts <= rtmax + rttol)]
+    deltas = np.diff(peak_range)
+    return max(deltas) + epsilon if len(deltas) else epsilon
+
+
+def _check_params(kwargs):
+    chrom, rtmin, rtmax, rttol = kwargs
+    cond1 = len(chrom) if chrom is not None else False
+    cond2 = [v is not None for v in [rtmin, rtmax, rttol]]
+    return cond1 and cond2
+
+
+def _set_windows(t, min_fwhm=2.0, rt_value_column=None):
+    params = [t.model_chromatogram, min_fwhm]
+    params.append(t[rt_value_column]) if rt_value_column else params.append(None)
+    t.add_column("temp", t.apply(adapt_window, *params), object)
+    t.add_column("_rtmin", t.apply(lambda v: v[0], t.temp), RtType)
+    t.add_column("_rtmax", t.apply(lambda v: v[1], t.temp), RtType)
+    t.replace_column(
+        "rtmin_chromatogram",
+        t._rtmin.is_not_none().then_else(t._rtmin, t.rtmin_chromatogram),
+        RtType,
+    )
+    t.replace_column(
+        "rtmax_chromatogram",
+        t._rtmax.is_not_none().then_else(t._rtmax, t.rtmax_chromatogram),
+        RtType,
+    )
+
+    t.drop_columns("temp", "_rtmin", "_rtmax")
+
+
+"""
+Bug only zero intensity values
+"""
+
+
+def adapt_window(model, min_fwhm, rt=None):
+    rts, ints = model.graph()
+    if not len(rts):
+        return None, None
+    smoothed = _get_smoothed(ints)
+    rt_ = _determine_rt(rts, smoothed)
+    rt = rt if rt_ is None else rt_
+    if rt is None:
+        return None, None
+    fwhm = _determine_fwhm(rts, smoothed, rt, min_fwhm)
+    f_asym = _determine_asymmetric_factor(rts, smoothed, rt)
+    left_pos = np.argwhere(np.logical_and(rts >= rt - 2 * f_asym * fwhm, rts < rt))
+    right_pos = np.argwhere(np.logical_and(rts <= rt + 2 / f_asym * fwhm, rts > rt))
+    start = _min_value_pos(left_pos, smoothed, False)
+    start = start if start else 0
+    stop = _min_value_pos(right_pos, smoothed)
+    stop = stop if stop else len(rts) - 1
+    return rts[start], rts[stop]
+
+
+def _min_value_pos(positions, intensities, rightside=True):
+
+    if len(positions):
+        i = np.where(intensities[positions] == min(intensities[positions]))
+        index = 0 if rightside else -1
+        return positions[i][index]
+
+
+def determine_rt(model, rt):
+    # rtmin, rtmax = limits
+    rts, ints = model.graph()
+    if len(ints):
+        smoothed = _get_smoothed(ints)
+        rt = _determine_rt(rts, smoothed)
+    return rt
+
+
+def _get_smoothed(values):
+    try:
+        smoothed = savgol_filter(values, 7, 3)
+        # we exclude negative intensity values
+        smoothed[smoothed < 0] = 0
+        return smoothed
+    except:
+        return values
+
+
+def _determine_rt(rts, smoothed):
+    i = np.where(smoothed == max(smoothed))[0]
+    i = int((min(i) + max(i)) / 2)
+    return rts[i]
+
+
+def _determine_asymmetric_factor(rts, smoothed, rt):
+    max_int = _determine_max_int(rt, rts, smoothed)
+    pos = np.where(np.logical_and(smoothed >= 0.2 * max_int, smoothed <= max_int))[0]
+    diff_pos = np.diff(pos)
+    check = np.where(diff_pos > 1)[0] + 1
+    blocks = np.split(pos, check)
+    i = np.where(abs(rts - rt) == np.min(abs(rts - rt)))[0]
+    for block in blocks:
+        if i in block:
+            left = len(block[block <= i])
+            right = len(block[block >= i])
+            return left / right
+    return 1.0
+
+
+def _determine_fwhm(rts, smoothed, rt, min_fwhm=2.0):
+    fwhm = min_fwhm
+    max_int = _determine_max_int(rt, rts, smoothed)
+    pos = np.where(np.logical_and(smoothed >= 0.5 * max_int, smoothed <= max_int))[0]
+    diff_pos = np.diff(pos)
+    check = np.where(diff_pos > 1)[0] + 1
+    blocks = np.split(pos, check)
+    i = np.where(abs(rts - rt) == np.min(abs(rts - rt)))[0]
+    for block in blocks:
+        if i in block:
+            fwhm = rts[max(block)] - rts[min(block)]
+    return fwhm if fwhm > min_fwhm else min_fwhm
+
+
+def _determine_max_int(rt, rts, ints):
+    diffs = abs(rts - rt)
+    pos = np.where(diffs == min(diffs))
+    return max(ints[pos])
+
+
+# ___________________ coeluting peaks ____________________
+# based on cosine similarity scoring
+
+
+def adapt_rt_by_coeluting_peaks(
+    t,
+    group_id_column="compound",
+    reference_column="is_coelution_reference_peak",
+    only_use_ref_peaks=True,
+    sample_wise=True,
+    min_fwhm=2.0,
+    **kwargs
+):
+    if len(t):
+        t.add_enumeration("rowid")
+        rid2algo = dict(zip(t.rowid, t.peak_shape_model_chromatogram))
+
+        # integration_algorithm = t_.peak_shape_model_chromatogram.unique_value()
+        temp_cols = "_rt_ref", "_fwhm_ref", "_ok", "_rtmin_ref", "_rtmax_ref", "rowid"
+        _add_rt_ref_columns(
+            t, reference_column, group_id_column, only_use_ref_peaks, sample_wise
+        )
+        t.add_column("_ok", (t.peak_coelutes == "ok").then_else(True, False), bool)
+        t_ok = t.filter(t._ok)
+        tables = [t_ok]
+        t_crit = t.filter(t._ok == False)
+        t.drop_columns(*temp_cols)
+        _move_rt_windows(t_crit, "sgolay", min_fwhm)
+        t_crit.replace_column(
+            "peak_shape_model_chromatogram",
+            t_crit.apply(rid2algo.get, t_crit.rowid),
+            str,
+        )
+        for t_ in t_crit.split_by_iter("peak_shape_model_chromatogram"):
+            algo = t_.peak_shape_model_chromatogram.unique_value()
+            integrate_chromatograms(t_, algo, in_place=True)
+            tables.append(t_)
+        t = Table.stack_tables(tables)
+        t.drop_columns(*temp_cols)
+    return t
+
+
+def _add_rt_ref_columns(
+    t, reference_column, group_col, only_use_ref_peaks, sample_wise
+):
+    group_cols = [t[group_col]]
+    if sample_wise:
+        group_cols.append(t.filename)
+
+    if only_use_ref_peaks:
+        assert reference_column is not None
+        t.add_column(
+            "_rt_ref",
+            t.group_by(*group_cols).aggregate(
+                _get_ref_rt, t.rt_chromatogram, t[reference_column]
+            ),
+            RtType,
+        )
+        t.add_column(
+            "_rtmin_ref",
+            t.group_by(*group_cols).aggregate(
+                _get_ref_rt, t.rtmin_chromatogram, t[reference_column]
+            ),
+            RtType,
+        )
+        t.add_column(
+            "_rtmax_ref",
+            t.group_by(*group_cols).aggregate(
+                _get_ref_rt, t.rtmax_chromatogram, t[reference_column]
+            ),
+            RtType,
+        )
+    else:
+        t.add_column(
+            "_rt_ref", t.group_by(*group_cols).median(t.rt_chromatogram), RtType
+        )
+        t.add_column(
+            "_rtmin_ref", t.group_by(*group_cols).median(t.rtmin_chromatogram), RtType
+        )
+        t.add_column(
+            "_rtmax_ref", t.group_by(*group_cols).median(t.rtmax_chromatogram), RtType
+        )
+    t.add_column("_fwhm_ref", (t._rtmax_ref - t._rtmin_ref) / 4, float)
+
+
+def _move_rt_windows(t, integration_algorithm, min_fwhm):
+    t.replace_column(
+        "rtmin_chromatogram",
+        t.rtmin_chromatogram + t._rt_ref - t.rt_chromatogram,
+        RtType,
+    )
+    t.replace_column(
+        "rtmax_chromatogram",
+        t.rtmax_chromatogram + t._rt_ref - t.rt_chromatogram,
+        RtType,
+    )
+
+    integrate_chromatograms(t, "linear", in_place=True)
+    _set_windows(t, min_fwhm, "_rt_ref")
+    # bug fix
+    # special case: zero len peaks: rmse calculation fails.
+    # we apply linear instead
+    try:
+        integrate_chromatograms(t, integration_algorithm, in_place=True)
+    except:
+        integrate_chromatograms(t, "linear", in_place=True)
+    t.add_or_replace_column(
+        "rt_chromatogram",
+        t.apply(determine_rt, t.model_chromatogram, t.rt_chromatogram),
+        RtType,
+    )
+
+
+def _get_ref_rt(rts, references):
+    rts_ = [rt for rt, ref in zip(rts, references) if ref]
+    return np.mean(rts_)

tadamz-0.13.0a1/src/tadamz/calibration/__init__.py

@@ -0,0 +1,6 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Jun 11 09:22:41 2024
+
+@author: pkiefer
+"""