klassez 0.1.1.dev0__tar.gz → 0.1.1.dev1__tar.gz

{klassez-0.1.1.dev0 → klassez-0.1.1.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: klassez
-Version: 0.1.1.dev0
+Version: 0.1.1.dev1
 Summary: A collection of functions for NMR data handling
 Author: Letizia Fiorucci
 Author-email: Francesco Bruno <bruno@cerm.unifi.it>

{klassez-0.1.1.dev0 → klassez-0.1.1.dev1}/klassez/Spectra.py

@@ -904,9 +904,9 @@ class Spectrum_1D:
         if filename is None:
             filename = self.datadir / self.filename
         if fvf:
-            filename_x = filename.with_suffix('.fvf')
+            filename_x = Path(filename).with_suffix('.fvf')
         else:
-            filename_x = filename.with_suffix('.ivf')
+            filename_x = Path(filename).with_suffix('.ivf')
 
         # If Hs is not given, sum the intensities
         if Hs is None:
@@ -1648,7 +1648,7 @@ class Spectrum_2D:
         if self.acqus['FnMODE'] in ['QF', 'QF-nofreq']:
             self.S = processing.hilbert(self.rr)
         else:
-            self.S = processing.repack_2D(processing.hilbert2(self.rr))
+            self.S = processing.repack_2D(*processing.hilbert2(self.rr))
 
         # Cut the frequency scales as well
         self.freq_f2 = misc.ppm2freq(self.ppm_f2, self.acqus['SFO2'], self.acqus['o2p'])
@@ -3390,7 +3390,9 @@ class Pseudo_2D(Spectrum_2D):
         """
         original = deepcopy(self.S)
         # Correct the baseline
-        datap = processing.abs_v2(self.ppm, self.r, self.acqus['SFO1'], n=n, lims=lims, alpha=alpha, winsize=winsize, qfil=qfil, qfilp=qfilp)
+        datap = np.empty_like(self.S)
+        for k, data in enumerate(self.rr):
+            datap[k] = processing.abs_v2(self.ppm_f2, data, self.acqus['SFO1'], n=n, lims=lims, alpha=alpha, winsize=winsize, qfil=qfil, qfilp=qfilp)
         # Retrieve imaginary part
         self.S = processing.hilbert(datap)
         return original - datap

{klassez-0.1.1.dev0 → klassez-0.1.1.dev1}/klassez/__init__.py

@@ -17,4 +17,4 @@ from .config import CM, CM_2D, COLORS, cron, safe_kws, textcolor, _print, cprint
 
 print = cprint
 
-__version__ = "0.1.1.dev0"
+__version__ = "0.1.1.dev1"

{klassez-0.1.1.dev0 → klassez-0.1.1.dev1}/klassez/anal.py

@@ -771,14 +771,7 @@ def integrate(ppm0, data0, SFO1, filename='integrals', X_label=r'$\delta\,$F1 /p
 
     def calc_bas(isx, idx):
         """ Compute straight line baseline """
-        # Two points
-        bas_points = np.array([data[isx], data[idx]])
-        # Use the linear regression to connect them, employ the point scale
-        _, (bas_m, bas_q) = fit.lr(bas_points, x=np.asarray([isx, idx]))
-        # full-length x-scale for baseline
-        xb = np.arange(isx, idx+1, 1)
-        # baseline = mx + q
-        bas = xb * bas_m + bas_q
+        bas = processing.sl_bas_onidx(data, (isx, idx))
         return bas
 
     def onselect(vsx, vdx):
@@ -1076,21 +1069,12 @@ def integrate_p2D(ppm0, data0, SFO1, ref=0, indirect_scale=None, filename='integ
 
     def calc_bas(y, isx, idx):
         """ Compute straight line baseline """
-        # Two points
-        bas_points = np.array([y[isx], y[idx]])
-        # Use the linear regression to connect them, employ the point scale
-        _, (bas_m, bas_q) = fit.lr(bas_points, x=np.asarray([isx, idx]))
-        # full-length x-scale for baseline
-        xb = np.arange(isx, idx+1, 1)
-        # baseline = mx + q
-        bas = xb * bas_m + bas_q
+        bas = processing.sl_bas_onidx(y, (isx, idx))
         return bas
 
     def calc_all_bas(isx, idx):
         """ Compute the straight line baseline for all the experiments """
-        all_bas = np.array([
-            calc_bas(y, isx, idx)
-            for y in all_data])
+        all_bas = processing.sl_bas_onidx(all_data, (isx, idx))
         return all_bas
 
     def axy_plot(y):

{klassez-0.1.1.dev0 → klassez-0.1.1.dev1}/klassez/figures.py

@@ -1341,7 +1341,7 @@ def stacked_plot(ppmscale, S, xlims=None, lw=0.5, X_label=r'$\delta\ $ F1 /ppm',
     print('Done.', c='tab:cyan')
 
 
-def dotmd(ppmscale, S, labels=None, lw=0.8, n_xticks=10):
+def dotmd(ppmscale, S, labels=None, lw=0.8, n_xticks=10, rev=True):
     """
     Interactive display of multiple 1D spectra.
 
@@ -1357,6 +1357,8 @@ def dotmd(ppmscale, S, labels=None, lw=0.8, n_xticks=10):
         Linewidth of the spectra plots
     n_xticks : int
         Number of numbered ticks on the x-axis of the figure
+    rev : bool
+        When ``True``, the x-scale goes from maximum (left) to minimum (right)
 
     Returns
     -------
@@ -1486,7 +1488,9 @@ def dotmd(ppmscale, S, labels=None, lw=0.8, n_xticks=10):
     # Auto-adjusts the limits for the y-axis
     misc.set_ylim(ax, np.concatenate(S))
     # Make pretty scales
-    misc.pretty_scale(ax, (np.max(np.concatenate(ppmscale)), np.min(np.concatenate(ppmscale))), axis='x', n_major_ticks=n_xticks)
+    misc.pretty_scale(ax, (np.min(np.concatenate(ppmscale)), np.max(np.concatenate(ppmscale))), axis='x', n_major_ticks=n_xticks)
+    if rev:
+        ax.set_xlim(ax.get_xlim()[::-1])
     misc.pretty_scale(ax, ax.get_ylim(), axis='y', n_major_ticks=10)
 
     # Pretty y-axis numbers

{klassez-0.1.1.dev0 → klassez-0.1.1.dev1}/klassez/fit.py

@@ -2398,7 +2398,7 @@ def make_iguess_auto(ppm, data, SW, SFO1, o1p, filename='iguess'):
     #  Initialize variables
     # Write the info on the file
     filename = Path(filename)
-    filename_x = filename.with_suffix('ivf')
+    filename_x = filename.with_suffix('.ivf')
     with filename_x.open('a', buffering=1) as f:
         now = datetime.now()
         date_and_time = now.strftime("%d/%m/%Y at %H:%M:%S")
@@ -3692,8 +3692,8 @@ class Voigt_Fit:
         # Filename check
         if filename is None:
             filename = f'{self.filename}'
-        filename += '_rhist'
         filename = Path(filename)
+        filename = Path(filename).with_name(filename.stem + '_rhist')
 
         # Select the correct object
         if what == 'iguess':
@@ -8109,9 +8109,10 @@ class DosyFit:
         # Set the filename, if not given
         if filename is None:
             filename = f'{self.filename}'
+        filename = Path(filename)
 
         # Make the directories
-        figure_path = Path(f'Figures_{filename}') / f'{what}'
+        figure_path = filename.with_name('Figures_' + filename.stem) / f'{what}'
         figure_path.mkdir(exist_ok=True, parents=True)
 
         # Make the figures

{klassez-0.1.1.dev0 → klassez-0.1.1.dev1}/klassez/processing.py

@@ -895,7 +895,7 @@ def fp(data, wf=None, zf=None, fcor=0.5, tdeff=0):
     """
     # Correct the shape of tdeff for pseudo_2D spectra, xf2, and stuff
     if len(data.shape) > 1 and not isinstance(tdeff, (list, tuple, np.ndarray)):
-        tdeff = [0 for w in len(data.shape)-1] + [tdeff]
+        tdeff = [0 for w in range(len(data.shape)-1)] + [tdeff]
     # Window function
     # Rectangle
     datap = processing.td_eff(data, tdeff)
@@ -2295,8 +2295,9 @@ def interactive_phase_1D(ppmscale, S, reference=None):
 
     def reset(event):
         # Reset the phase and pivot values to their starting point
-        nonlocal P
-        P = np.array([0, 0, round(np.mean([min(ppmscale), max(ppmscale)]))])
+        nonlocal P, sens
+        P = np.array([0, 0, round(np.mean(ppmscale), 2)])
+        sens = [5, 5, 0.1]
         on_scroll(event)
 
     def save(event):
@@ -2805,20 +2806,6 @@ def integral(fx, x=None, dx=None, lims=None, use_bas=False):
 
         :func:`klassez.misc.trim_data`
     """
-    def calc_bas(y, isx, idx):
-        """ Compute straight line baseline """
-        # Two points
-        bas_points = np.array([y[..., isx], y[..., idx]])
-        # Use the linear regression to connect them, employ the point scale
-        bas = []
-        for k, tr in enumerate(bas_points):
-            _, (bas_m, bas_q) = fit.lr(bas_points, x=np.asarray([isx, idx]))
-            # full-length x-scale for baseline
-            xb = np.arange(isx, idx+1, 1)
-            # baseline = mx + q
-            bas.append(xb * bas_m + bas_q)
-        return np.array(bas)
-
     # Copy variables for check
     fx_in = np.copy(fx)
     if x is None:   # Make the point scale
@@ -2836,7 +2823,7 @@ def integral(fx, x=None, dx=None, lims=None, use_bas=False):
         x_tr, fx_tr = misc.trim_data(x_in, fx_in, lims)
 
     if use_bas:
-        bas = calc_bas(fx_tr, 0, len(x_tr)-1)
+        bas = processing.sl_bas_onidx(fx_tr, (0, len(x_tr)-1))
     else:
         bas = np.zeros_like(x_tr)
 
@@ -4980,7 +4967,7 @@ def stack_fids(*fids, filename=None):
     p2d = np.stack(p2d_fid, axis=0)
 
     # Save the .npy file
-    if isinstance(filename, str):
+    if isinstance(filename, (str, Path)):
         np.save(filename, p2d)
 
     return p2d
@@ -6092,3 +6079,99 @@ def extend_taq(old_taq, newsize=None):
         dw = misc.calcres(old_taq)      # Get the dwell time
         new_taq = np.arange(0, dw * newsize, dw)    # Compute new scale
     return new_taq
+
+
+def sl_bas_onidx(y, x_idx):
+    """
+    Computes the straight line that connects ``y[min(x_idx)]`` with ``y[max(x_idx)]``.
+    If ``y`` is a 2darray, a 2darray of lines is returned, one correspondant to each row of ``y``.
+    The lines will be ``max(x_idx) - min(x_idx)`` points long.
+
+    Parameters
+    ----------
+    y : 1darray or 2darray
+        Array for which to compute the connecting lines
+    x_idx : tuple
+        Points indices of the endpoints of the connecting lines
+
+    Returns
+    -------
+    bas : 1darray or 2darray
+        Computed connecting lines. Of note, this is squeezed before returning!
+
+    .. seealso::
+
+        :func:`numpy.squeeze`
+        :func:`klassez.fit.lr`
+    """
+    # Let's be sure the indices are in the correct order
+    x_idx = sorted(x_idx)
+    # Array of shape (y.shape[0], 2) of the endpoints
+    bas_points = np.array([y[..., q] for q in x_idx]).T
+    if len(bas_points.shape) == 1:  # add a dimension to use the for after
+        bas_points = [bas_points]
+
+    bas = []    # placeholder
+    # Loop on the rows of the endpoints
+    for k, tr in enumerate(bas_points):
+        # tr contains two points -> only one line exists
+        _, (bas_m, bas_q) = fit.lr(tr, x=np.asarray(x_idx))
+        # Compute the scale for rendering the connecting line correctly
+        xb = np.arange(min(x_idx), max(x_idx) + 1)
+        # Add to placeholder
+        bas.append(xb * bas_m + bas_q)
+    # Remove the extra dimension added before, if needed
+    return np.squeeze(np.array(bas))
+
+
+def sl_bas(x, y, lims=None):
+    """
+    Computes the straight line that connects ``y`` between ``lims`` on the ``x`` scale.
+    If ``y`` is a 2darray, a 2darray of lines is returned, one correspondant to each row of ``y``.
+
+    Parameters
+    ----------
+    y : 1darray or 2darray
+        Array for which to compute the connecting lines
+    x : 1darray
+        Scale for the referencing of ``lims``
+    lims : tuple
+        ``(left, right)`` for selecting the endpoints
+
+    Returns
+    -------
+    bas_overlay : 1darray or 2darray
+        Computed connecting lines, with the same shape of ``y``. Of note, this is squeezed before returning!
+
+    .. seealso::
+
+        :func:`numpy.squeeze`
+        :func:`klassez.processing.sl_bas_onidx`
+    """
+    # Get the correct arrays to work with
+    if lims is None:
+        # Use the whole data
+        x_tr = deepcopy(x)
+        y_tr = deepcopy(y)
+        # Limits are therefore first and last point of the scale
+        lims = x[0], x[-1]
+    else:
+        # Cut the data according to lims
+        if len(y.shape) > 1:
+            # Use a dummy yscale to cut only on the last dimension
+            x_tr, _, y_tr = misc.trim_data_2D(x, np.arange(y.shape[0]), y, xlim=lims)
+        else:
+            # Just cut
+            x_tr, y_tr = misc.trim_data(x, y, lims=lims)
+
+    # Get the indices of the endpoints ON x NOT xtrim, otherwise the overlay does not work
+    x_idx = [misc.ppmfind(x, v)[0] for v in lims]
+    # Compute the correcting lines
+    bas = sl_bas_onidx(y, x_idx)
+    # Add a dimension to still use the for
+    if len(bas.shape) == 1:
+        bas = [bas]
+
+    # Match the shape of y. Use always the left limit as anchor point
+    overlay_bas = [misc.sum_overlay(np.zeros_like(x), y_b, x[min(x_idx)], x) for y_b in bas]
+    return np.squeeze(np.array(overlay_bas))

{klassez-0.1.1.dev0 → klassez-0.1.1.dev1}/klassez/sim.py

@@ -134,9 +134,7 @@ def load_sim_1D(File):
     dic : dict
         Dictionary of the parameters, ready to be read from the simulation functions.
     """
-
-    with open(File, 'r') as f:
-        inp = f.readlines()
+    inp = Path(File).read_text().splitlines(keepends=True)
     keys = []
     vals = []
     for i in range(len(inp)):
@@ -201,7 +199,7 @@ def sim_1D(File, pv=False):
     fid : 1darray
         FID of the simulated spectrum.
     """
-    if isinstance(File, str):
+    if isinstance(File, (str, Path)):
         in_file = load_sim_1D(File)
     elif isinstance(File, dict):
         in_file = File
@@ -247,8 +245,7 @@ def load_sim_2D(File, states=True):
     dic : dict
         Dictionary of the parameters, ready to be read from the simulation functions.
     """
-    with open(File, 'r') as f:
-        inp = f.readlines()
+    inp = Path(File).read_text().splitlines(keepends=True)
     keys = []
     vals = []
     for i in range(len(inp)):
@@ -320,7 +317,7 @@ def sim_2D(File, states=True, alt=True, pv=False):
     """
 
     # Generates a dictionary of parameters from an input file
-    if isinstance(File, str):
+    if isinstance(File, (str, Path)):
         in_file = sim.load_sim_2D(File, states=states)
     elif isinstance(File, dict):
         in_file = File

{klassez-0.1.1.dev0 → klassez-0.1.1.dev1}/klassez.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: klassez
-Version: 0.1.1.dev0
+Version: 0.1.1.dev1
 Summary: A collection of functions for NMR data handling
 Author: Letizia Fiorucci
 Author-email: Francesco Bruno <bruno@cerm.unifi.it>

{klassez-0.1.1.dev0 → klassez-0.1.1.dev1}/klassez.egg-info/SOURCES.txt

@@ -5,8 +5,6 @@ pyproject.toml
 setup.cfg
 docs/Makefile
 docs/make.bat
-docs/rebuild_kz.err
-docs/rebuild_kz.log
 docs/requirements.txt
 klassez/Spectra.py
 klassez/__init__.py

klassez-0.1.1.dev0/docs/rebuild_kz.err

@@ -1,5 +0,0 @@
-* Creating isolated environment: venv+pip...
-* Installing packages in isolated environment:
-  - setuptools>=61.0
-* Getting build dependencies for sdist...
-* Building sdist...

klassez-0.1.1.dev0/docs/rebuild_kz.log

@@ -1,36 +0,0 @@
-running egg_info
-writing klassez.egg-info/PKG-INFO
-writing dependency_links to klassez.egg-info/dependency_links.txt
-writing requirements to klassez.egg-info/requires.txt
-writing top-level names to klassez.egg-info/top_level.txt
-reading manifest file 'klassez.egg-info/SOURCES.txt'
-reading manifest template 'MANIFEST.in'
-adding license file 'LICENSE.txt'
-writing manifest file 'klassez.egg-info/SOURCES.txt'
-running sdist
-running egg_info
-writing klassez.egg-info/PKG-INFO
-writing dependency_links to klassez.egg-info/dependency_links.txt
-writing requirements to klassez.egg-info/requires.txt
-writing top-level names to klassez.egg-info/top_level.txt
-reading manifest file 'klassez.egg-info/SOURCES.txt'
-reading manifest template 'MANIFEST.in'
-adding license file 'LICENSE.txt'
-writing manifest file 'klassez.egg-info/SOURCES.txt'
-running check
-creating klassez-0.1.1.dev0
-creating klassez-0.1.1.dev0/docs
-creating klassez-0.1.1.dev0/klassez
-creating klassez-0.1.1.dev0/klassez.egg-info
-creating klassez-0.1.1.dev0/klassez/tables
-creating klassez-0.1.1.dev0/test
-copying files to klassez-0.1.1.dev0...
-copying LICENSE.txt -> klassez-0.1.1.dev0
-copying MANIFEST.in -> klassez-0.1.1.dev0
-copying README.md -> klassez-0.1.1.dev0
-copying pyproject.toml -> klassez-0.1.1.dev0
-copying setup.cfg -> klassez-0.1.1.dev0
-copying docs/Makefile -> klassez-0.1.1.dev0/docs
-copying docs/make.bat -> klassez-0.1.1.dev0/docs
-copying docs/rebuild_kz.err -> klassez-0.1.1.dev0/docs
-copying docs/rebuild_kz.log -> klassez-0.1.1.dev0/docs