Project management

from pathlib import Path

[1]:

from spectrochempy import NDDataset
from spectrochempy import Project
from spectrochempy import pathclean
from spectrochempy import preferences as prefs

SpectroChemPy's API - v.0.7.1
© Copyright 2014-2025 - A.Travert & C.Fernandez @ LCS

Project creation

We can easily create a new project to store various datasets

[2]:

proj = Project()

As we did not specify a name, a name has been attributed automatically:

[3]:

proj.name

[3]:

'Project-Project_c94b923e'

To get the signature of the object, one can use the usual ‘?’. Uncomment the following line to check

[4]:

# Project?

Let’s change this name

[5]:

proj.name = "myNMRdata"
proj

[5]:

Project myNMRdata:
(empty project)

Now we will add a dataset to the project.

First we read the dataset (here some NMR data) and we give it some name (e.g. ‘nmr n°1’)

[6]:

datadir = pathclean(prefs.datadir)
path = datadir / "nmrdata" / "bruker" / "tests" / "nmr"
nd1 = NDDataset.read_topspin(
    path / "topspin_1d", expno=1, remove_digital_filter=True, name="NMR_1D"
)
nd2 = NDDataset.read_topspin(
    path / "topspin_2d", expno=1, remove_digital_filter=True, name="NMR_2D"
)

 WARNING | (UserWarning) (196608,)cannot be shaped into(147, 1024)

To add it to the project, we use the add_dataset function for a single dataset:

[7]:

proj.add_datasets(nd1)

or add_datasets for several datasets.

[8]:

proj.add_datasets(nd1, nd2)

Display its structure

[9]:

proj

[9]:

Project myNMRdata:
⤷ NMR_1D (dataset)
⤷ NMR_2D (dataset)

It is also possible to add other projects as sub-project (using the add_project )

Remove an element from a project

[10]:

proj.remove_dataset("NMR_1D")
proj

[10]:

Project myNMRdata:
⤷ NMR_2D (dataset)

Get project’s elements

[11]:

proj.add_datasets(nd1, nd2)
proj

[11]:

Project myNMRdata:
⤷ NMR_1D (dataset)
⤷ NMR_2D (dataset)

We can just use the name of the element as a project attribute.

[12]:

proj.NMR_1D

[12]:

name	NMR_1D
author	runner@fv-az1774-299
created	2025-02-25 08:01:58+00:00
DATA
title	intensity
values	R[ 1078 2284 ... 0.2342 -0.1008] pp I[ -1037 -2200 ... 0.06203 -0.05273] pp
size	12411 (complex)
DIMENSION `x`
size	12411
title	F1 acquisition time
coordinates	[ 0 4 ... 4.964e+04 4.964e+04] µs

[13]:

_ = proj.NMR_1D.plot()

../../../_images/userguide_objects_project_project_25_0.png

However, this work only if the name contains no space, dot, comma, colon, etc. The only special character allowed is the underscore _ . If the name is not respecting this, then it is possible to use the following syntax (as a project behave as a dictionary). For example:

[14]:

proj["NMR_1D"].data

[14]:

array([1.08e+03-1.04e+03j, 2.28e+03-2.2e+03j, ...,    0.234+0.062j,   -0.101-0.0527j])

[15]:

proj.NMR_2D

[15]:

name	NMR_2D
author	runner@fv-az1774-299
created	2025-02-25 08:01:58+00:00
DATA
title	intensity
values	RR[[ -0.2238 -0.1985 ... -0.1662 0.03262] [-0.006566 0.0282 ... -0.02949 -0.06717] ... [ 0 0 ... 0 0] [ 0 0 ... 0 0]] pp RI[[ 0.06219 0.1467 ... 0.04565 0.03068] [-0.05969 -0.08752 ... -0.05134 -0.05994] ... [ -0 -0 ... -0 -0] [ -0 -0 ... -0 -0]] pp IR[[ -0.1623 -0.0563 ... 0.02654 -0.01094] [ 0.1344 -0.006515 ... -0.08239 0.00516] ... [ 0 0 ... 0 0] [ 0 0 ... 0 0]] pp II[[-0.003312 -0.001535 ... 0.02067 -0.08058] [-0.05685 0.1174 ... 0.05831 -0.003414] ... [ -0 -0 ... -0 -0] [ -0 -0 ... -0 -0]] pp
shape	(y:96(complex), x:948(complex))
DIMENSION `x`
size	948
title	F2 acquisition time
coordinates	[ 0 48 ... 4.541e+04 4.546e+04] µs
DIMENSION `y`
size	96
title	F1 acquisition time
coordinates	[ 0 74 ... 6956 7030] µs

Saving and loading projects

[16]:

proj

[16]:

Project myNMRdata:
⤷ NMR_1D (dataset)
⤷ NMR_2D (dataset)

Saving

[17]:

proj.save_as("NMR")

[17]:

PosixPath('/home/runner/work/spectrochempy/spectrochempy/docs/sources/userguide/objects/project/NMR.pscp')

Loading

[18]:

proj2 = Project.load("NMR")

[19]:

proj2

[19]:

Project NMR:
⤷ NMR_1D (dataset)
⤷ NMR_2D (dataset)

[20]:

_ = proj2.NMR_1D.plot()

../../../_images/userguide_objects_project_project_36_0.png

[21]:

proj2.NMR_2D

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
File ~/work/spectrochempy/spectrochempy/.venv/lib/python3.10/site-packages/IPython/core/formatters.py:406, in BaseFormatter.__call__(self, obj)
    404     method = get_real_method(obj, self.print_method)
    405     if method is not None:
--> 406         return method()
    407     return None
    408 else:

File ~/work/spectrochempy/spectrochempy/src/spectrochempy/core/dataset/baseobjects/ndarray.py:857, in NDArray._repr_html_(self)
    856 def _repr_html_(self):
--> 857     return convert_to_html(self)

File ~/work/spectrochempy/spectrochempy/src/spectrochempy/utils/print.py:112, in convert_to_html(obj)
    102 tr = (
    103     "<tr>"
    104     "<td style='padding-right:5px; padding-bottom:0px; "
   (...)
    107     "padding-top:0px; {2} '>{1}</td><tr>\n"
    108 )
    110 obj._html_output = True
--> 112 out = obj._cstr()
    114 regex = r"\0{3}[\w\W]*?\0{3}"
    116 # noinspection PyPep8

File ~/work/spectrochempy/spectrochempy/src/spectrochempy/core/dataset/nddataset.py:592, in NDDataset._cstr(self)
    588 out += f"       author: {self.author}\n"
    589 out += f"      created: {self.created}\n"
    590 out += (
    591     f"     modified: {self.modified}\n"
--> 592     if (self._modified - self._created).seconds > 30
    593     else ""
    594 )
    596 wrapper1 = textwrap.TextWrapper(
    597     initial_indent="",
    598     subsequent_indent=" " * 15,
    599     replace_whitespace=True,
    600     width=self._text_width,
    601 )
    603 pars = self.description.strip().splitlines()

TypeError: can't subtract offset-naive and offset-aware datetimes

[21]:

NDDataset: [quaternion] pp (shape: (y:96, x:948))

[22]:

_ = proj.NMR_2D.plot()

../../../_images/userguide_objects_project_project_38_0.png

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