separated from previous projects

.gitignore

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+*.egg-info/
+dist/*
+*.pyc
+.ipynb_checkpoints
+.vscode

README.md

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+# igor-tools
+
+Simple tools to manage IGOR Pro `.itx` files.
+
+See `example.ipynb` for usage.

example_files/example_out.itx

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+IGOR
+WAVES/N=(6, 7)  example_output
+BEGIN
+1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 
+1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 
+1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 
+1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 
+1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 
+1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 
+END
+X SetScale/P x 0.0,0.1, "m", example_output;
+X SetScale/P y 0.0,0.2, "m", example_output;

igor_tools/__init__.py

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+import traceback
+
+from . import igor
+
+from .igor import Wave, Wave1d, Wave2d
+
+__version__ = "0.1.0"
+
+
+def read_itx(fname):
+    """
+    Returns the list of igor waves that are included in the .itx file 
+    """
+    f=open(fname, 'r')
+    lines=f.readlines()
+    f.close()
+
+    line = lines.pop(0).strip()
+    if not line == "IGOR":
+        raise IOError("Files does not begin with 'IGOR'")
+
+    waves = []
+    while len(lines) != 0:
+        try:
+            wave = igor.read_wave(lines)
+            if wave is not None:
+                waves.append(wave)
+        except Exception:
+            traceback.print_exc()
+
+    return waves
+
+def write_2d_itx(fname, data, xaxis, yaxis, wavename):
+    """
+    Write a 2-dimensional data as .itx file
+
+    Args:
+        fname: Name of the output file
+        data: the 2d data
+        xaxis: iterable containing (x_min, x_delta, unit)
+        yaxis: iterable containing (y_min, y_delta, unit)
+        wavename: name of the igor wave
+    """
+
+    x = igor.Axis('x', xaxis[0], xaxis[1], xaxis[2], wavename)
+    y = igor.Axis('y', yaxis[0], yaxis[1], yaxis[2], wavename)
+
+    wave = Wave2d(
+            data=data,
+            axes=[x,y],
+            name=wavename,
+        )
+
+    wave.write(fname)
+

igor_tools/igor.py

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+"""Classes for use with IGOR Pro
+
+Partially based on asetk module by Leopold Talirz
+(https://github.com/ltalirz/asetk/blob/master/asetk/format/igor.py)
+"""
+
+import re
+import numpy as np
+
+def read_wave(lines):
+    """
+    Reads the next wave section from the inputted list of lines
+    Parsed lines are removed from the list, allowing for subsequent calls
+    """
+
+    line = lines.pop(0)
+    while not re.match("WAVES",line):
+        if len(lines) == 0:
+            return None
+        line = lines.pop(0)
+    # 1d or 2d?
+    d2 = False
+    if "N=" in line:
+        d2 = True
+        match = re.search("WAVES/N=\(([\d, ]+)\)",line)
+        grid = match.group(1).split(',')
+        grid = np.array(grid, dtype=int)
+        name = line.split(")")[-1].strip()
+    else:
+        name = line.split()[-1]
+
+    line = lines.pop(0).strip()
+    if not line == "BEGIN":
+        raise IOError("Missing 'BEGIN' statement of data block")
+
+    # read data
+    datastring = ""
+    line = lines.pop(0)
+    while not re.match("END",line):
+        if len(lines) == 0:
+            return None
+        if line.startswith("X"):
+            return None
+        datastring += line
+        line = lines.pop(0)
+    data = np.array(datastring.split(), dtype=float)
+    if d2:
+        data = data.reshape(grid)
+
+    # read axes
+    axes = []
+    line = lines.pop(0)
+    matches = re.findall("SetScale.+?(?:;|$)", line)
+    for match in matches:
+        ax = Axis(None,None,None,None)
+        ax.read(match)
+        axes.append(ax)
+
+    if d2:
+        # read also the second axis
+        # is this necessary? can there be 2 lines with "SetScale" ?
+        line = lines.pop(0)
+        matches = re.findall("SetScale.+?(?:;|$)", line)
+        for match in matches:
+            ax = Axis(None,None,None,None)
+            ax.read(match)
+            axes.append(ax)
+        return Wave2d(data, axes, name)
+
+    return Wave1d(data, axes, name)
+
+
+class Axis(object):
+    """Represents an axis of an IGOR wave"""
+
+    def __init__(self, symbol, min_, delta, unit, wavename=None):
+        self.symbol = symbol
+        self.min = min_
+        self.delta = delta
+        self.unit = unit
+        self.wavename = wavename
+
+    def __str__(self):
+        """Prints axis in itx format
+        Note: SetScale/P expects minimum value and step-size
+        """
+        delta = 0 if self.delta is None else self.delta
+        s = "X SetScale/P {symb} {min},{delta}, \"{unit}\", {name};\n"\
+              .format(symb=self.symbol, min=self.min, delta=delta,\
+                      unit=self.unit, name=self.wavename)
+        return s
+
+    def read(self, string):
+        """Read axis from string
+        Format: 
+        X SetScale/P x 0,2.01342281879195e-11,"m", data_00381_Up;
+        SetScale d 0,0,"V", data_00381_Up
+        """
+        match = re.search("SetScale/?P? (.) ([+-\.\de]+),([+-\.\de]+),[ ]*\"(.*)\",\s*(\S+)", string)
+        self.symbol = match.group(1)
+        self.min = float(match.group(2))
+        self.delta = float(match.group(3))
+        self.unit = match.group(4)
+        self.wavename = match.group(5)
+        if self.wavename.endswith(';'):
+            self.wavename = self.wavename[:-1]
+
+
+class Wave(object):
+    """A class for IGOR waves"""
+
+    def __init__(self, data, axes, name=None):
+        """Initialize IGOR wave of generic dimension"""
+        self.data = data
+        self.axes = axes
+        self.name = "PYTHON_IMPORT" if name is None else name
+        self.dim = len(self.data.shape)
+
+    def __str__(self):
+        """Print IGOR wave"""
+        s = ""
+        s += "IGOR\n"
+
+        dimstring = "("
+        for i in range(len(self.data.shape)):
+            dimstring += "{}, ".format(self.data.shape[i])
+        dimstring = dimstring[:-2] + ")" 
+
+        s += "WAVES/N={}  {}\n".format(dimstring, self.name)
+        s += "BEGIN\n"
+        s += self.print_data()
+        s += "END\n"
+        for ax in self.axes:
+            s += str(ax)
+        return s
+
+    @property
+    def extent(self):
+        """Returns extent for plotting"""
+        grid = self.data.shape
+        extent = []
+        for i in range(len(grid)):
+            ax = self.axes[i]
+            extent.append(ax.min)
+            extent.append(ax.min+ax.delta*grid[i])
+
+        return np.array(extent)
+
+    @property
+    def x_min(self):
+        return self.axes[0].min
+
+    @property
+    def dx(self):
+        return self.axes[0].delta
+
+    @property
+    def x_max(self):
+        return self.x_min + self.dx * self.data.shape[0]
+
+    @property
+    def x_arr(self):
+        return self.x_min + np.arange(0, self.data.shape[0])*self.dx
+
+    @property
+    def x_symbol(self):
+        return self.axes[0].symbol
+
+    @property
+    def x_unit(self):
+        return self.axes[0].unit
+
+    def print_data(self):
+        """Determines how to print the data block.
+        
+        To be reimplemented by subclasses."""
+        pass
+
+    def write(self, fname):
+        f=open(fname, 'w')
+        f.write(str(self))
+        f.close()
+
+    def csv_header(self):
+        header = ""
+        shape = self.data.shape
+        for i_ax in range(len(shape)):
+            ax = self.axes[i_ax]
+            if header != "":
+                header += "\n"
+            header += "axis %d: %s [unit: %s] [%.6e, %.6e], delta=%.6e, n=%d" % (
+                i_ax, ax.symbol, ax.unit, ax.min, ax.min+ax.delta*(shape[i_ax]-1), ax.delta, shape[i_ax]
+            )
+        return header
+
+    def write_csv(self, fname, fmt="%.6e"):
+        np.savetxt(fname, self.data, delimiter=",", header=self.csv_header(), fmt=fmt)
+
+
+class Wave1d(Wave):
+    """1d Igor wave"""
+
+    def __init__(self, data, axes, name="1d"):
+        """Initialize 1d IGOR wave"""
+        super().__init__(data, axes, name)
+
+    def print_data(self):
+        """Determines how to print the data block"""
+        s = ""
+        for line in self.data:
+            s += "{:12.6e}\n".format(float(line))
+        return s
+
+
+class Wave2d(Wave):
+    """2d Igor wave"""
+
+    def __init__(self, data, axes, name="2d"):
+        """Initialize 2d IGOR wave"""
+        super().__init__(data, axes, name)
+
+    def print_data(self):
+        """Determines how to print the data block"""
+        s = ""
+        for line in self.data:
+            for x in line:
+                s += "{:12.6e} ".format(x)
+            s += "\n"
+        return s
+
+    @property
+    def y_min(self):
+        return self.axes[1].min
+
+    @property
+    def dy(self):
+        return self.axes[1].delta
+
+    @property
+    def y_max(self):
+        return self.y_min + self.dy * self.data.shape[1]
+
+    @property
+    def y_arr(self):
+        return self.y_min + np.arange(0, self.data.shape[1])*self.dy
+
+    @property
+    def y_symbol(self):
+        return self.axes[1].symbol
+
+    @property
+    def y_unit(self):
+        return self.axes[1].unit

setup.py

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+import setuptools
+
+with open("README.md", "r") as fh:
+    long_description = fh.read()
+
+setuptools.setup(
+    name="igor-tools",
+    version="0.1.0",
+    description="Simple tools to manage IGOR Pro .itx files",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    url="https://github.com/nanotech-empa",
+    packages=setuptools.find_packages(),
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: OS Independent",
+    ],
+    python_requires='>=3.6',
+    install_requires=[
+        "numpy",
+    ],
+)