From b14fda5cba090d29c4791b628d8e3977d74022cd Mon Sep 17 00:00:00 2001
From: wolfwiddra <wolf.widdra@physik.uni-halle.de>
Date: Mon, 16 Nov 2020 19:15:41 +0100
Subject: [PATCH] dielectrics bulk loss corrected

---
 Examples/startHREELS_Browser.py |   4 +-
 libhreels/__init__.py           |   2 +-
 libhreels/analysizeData.py      |  45 +++
 libhreels/calcHREELS.py         |   5 +-
 libhreels/dielectrics.py        |  14 +-
 poetry.lock                     | 559 ++++++++++++++++----------------
 pyproject.toml                  |   2 +-
 7 files changed, 345 insertions(+), 286 deletions(-)
 create mode 100644 libhreels/analysizeData.py

diff --git a/Examples/startHREELS_Browser.py b/Examples/startHREELS_Browser.py
index 9e8701e..fdf46bc 100644
--- a/Examples/startHREELS_Browser.py
+++ b/Examples/startHREELS_Browser.py
@@ -3,7 +3,7 @@ import sys
 import matplotlib.pyplot as plt
 import numpy as np
 
-datapath = "./data"
-# datapath = "./Examples/data"
+# datapath = "./data"
+datapath = "./Examples/data"
 
 ViewHREELS.runViewer(datapath=datapath, startWithFile='c1a03')
\ No newline at end of file
diff --git a/libhreels/__init__.py b/libhreels/__init__.py
index e13bd59..6849410 100644
--- a/libhreels/__init__.py
+++ b/libhreels/__init__.py
@@ -1 +1 @@
-__version__ = "1.0.8"
+__version__ = "1.1.0"
diff --git a/libhreels/analysizeData.py b/libhreels/analysizeData.py
new file mode 100644
index 0000000..5184c1e
--- /dev/null
+++ b/libhreels/analysizeData.py
@@ -0,0 +1,45 @@
+import numpy as np
+from matplotlib import pyplot as plt
+
+def findPeriod(list, period):
+    '''For a list of times (relative to a sync pulse) calculate the average time deviation squared.  
+    '''
+    residuum = []
+    sum_residuum = 0
+    for each in list:
+        r = each % period
+        residuum.append(r)
+        sum_residuum += r
+    av_res = sum_residuum / len(list)
+    deviation = 0
+    for res in residuum:
+        deviation += (res - av_res)**2
+    deviation /= (len(residuum)*period**2)
+    return deviation, av_res
+
+def makeTimeRelative(times, durations):
+    list = []
+    synced = False
+    t_zero = 0
+    for each in pulses:
+        if synced:
+            list.append(pulses[each][0]-t_zero)
+        if 9000 < pulses[each][2] < 9800:
+            print("synced")
+            t_zero = pulses[each][0]
+            synced = True
+    return list
+
+data = []       # read dat from file [[time in microsec, low duration, high duration], [...], ...]
+with open("data433_Signal2.txt", 'r') as f:
+    for line in f:
+        data.append([int(each) for each in line.split(',')])
+
+sumOn = 0; sumOff = 0
+for pulse in data[1:]:
+    sumOn += pulse[2]
+    sumOff += pulse[1]
+sumOn /= len(data)
+sumOff /= len(data)
+
+print("Average on and off times:", sumOn, sumOff)
diff --git a/libhreels/calcHREELS.py b/libhreels/calcHREELS.py
index 7e17da5..aa5f0e1 100644
--- a/libhreels/calcHREELS.py
+++ b/libhreels/calcHREELS.py
@@ -46,7 +46,7 @@ except:
 
 class lambin:
     def __init__(self, film, setup=setup, instrument=instrument):
-        if not sys.version.startswith('3.6'):
+        if not (sys.version.startswith('3.6') or sys.version.startswith('3.8')):
             print('''Make sure the Fortran routines 'myEels2' and 'myBoson' 
             have been complied with the proper f2py3 for the right 
             python version!!''') 
@@ -124,7 +124,8 @@ class lambin:
             emin,emax,wmin,wmax,loss_array,self.debug,len(loss_array))
         if normalized:
             norm = max(spectrum[:n])
-        return xOut[:n], spectrum[:n]/norm
+        # return xOut[:n], spectrum[:n]/norm
+        return xOut[:len(x)], spectrum[:len(x)]/norm
 
     def calcEps(self, x):
         epsArray = []
diff --git a/libhreels/dielectrics.py b/libhreels/dielectrics.py
index 82625c8..e50a856 100644
--- a/libhreels/dielectrics.py
+++ b/libhreels/dielectrics.py
@@ -18,7 +18,7 @@ def doping2surfacePlasma(doping,epsInfinity=1.):
     return np.sqrt(doping)*1.8817885780819758e-06/np.sqrt(1+epsInfinity)
 
 def loss(eps):
-    return -np.imag(eps)
+    return np.imag(1/eps)
 
 def surfaceLoss(eps):
     return np.imag(1/(1+eps))
@@ -28,14 +28,13 @@ def reflectivity(eps):  # IR reflectivity
     a =np.abs((sq-1)/(sq+1))
     return a*a
 
-def sigma(eps,w):       # Complex conductivity (ignored factor eps_0)
-    return (eps-1)*w/1j
+def sigma(eps,w,eps_Infinity=1):       # Complex conductivity 
+    return np.imag((eps-eps_Infinity)*w)
 
 def plotDielectrics(x,eps):
-    fig, axs = plt.subplots(3, 1, sharex=True)
-    axs[0].plot(x, loss(eps), label='Loss function')
-    axs[0].plot(x, np.real(eps), label='Re( $\epsilon (\omega )$ )')
-    axs[0].legend()
+    fig, axs = plt.subplots(3, 1, sharex=True, figsize=(6,6))
+    axs[0].plot(x, -np.imag(eps), label='-Im $\epsilon (\omega )$')
+    axs[0].plot(x, np.real(eps), label='Re $\epsilon (\omega )$')    axs[0].legend()
     axs[0].set_ylabel('Dielectric Function')
 
     axs[1].plot(x, surfaceLoss(eps), lineStyle='-')    
@@ -49,7 +48,6 @@ def plotDielectrics(x,eps):
     axs[0].set_xlim(left=0, right=max(x))
 
     plt.show()
-
 class oscillator:
     def __init__(self, wTO, wLO, gammaTO=20, gammaLO=20):
         self.wTO = wTO
diff --git a/poetry.lock b/poetry.lock
index 33cffd8..9cf2e39 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,252 +1,223 @@
 [[package]]
-category = "main"
-description = "Python command-line parsing library"
 name = "argparse"
+version = "1.4.0"
+description = "Python command-line parsing library"
+category = "main"
 optional = false
 python-versions = "*"
-version = "1.4.0"
 
 [[package]]
-category = "dev"
-description = "Atomic file writes."
-marker = "sys_platform == \"win32\""
 name = "atomicwrites"
+version = "1.4.0"
+description = "Atomic file writes."
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "1.4.0"
 
 [[package]]
-category = "dev"
-description = "Classes Without Boilerplate"
 name = "attrs"
+version = "20.2.0"
+description = "Classes Without Boilerplate"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "19.3.0"
 
 [package.extras]
-azure-pipelines = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "pytest-azurepipelines"]
-dev = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "sphinx", "pre-commit"]
-docs = ["sphinx", "zope.interface"]
-tests = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"]
+dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "sphinx", "sphinx-rtd-theme", "pre-commit"]
+docs = ["sphinx", "sphinx-rtd-theme", "zope.interface"]
+tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"]
+tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six"]
 
 [[package]]
-category = "main"
-description = "Python package for providing Mozilla's CA Bundle."
 name = "certifi"
+version = "2020.6.20"
+description = "Python package for providing Mozilla's CA Bundle."
+category = "main"
 optional = false
 python-versions = "*"
-version = "2020.4.5.1"
 
 [[package]]
-category = "main"
-description = "Universal encoding detector for Python 2 and 3"
 name = "chardet"
+version = "3.0.4"
+description = "Universal encoding detector for Python 2 and 3"
+category = "main"
 optional = false
 python-versions = "*"
-version = "3.0.4"
 
 [[package]]
-category = "dev"
-description = "Cross-platform colored terminal text."
-marker = "sys_platform == \"win32\""
 name = "colorama"
+version = "0.4.4"
+description = "Cross-platform colored terminal text."
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-version = "0.4.3"
 
 [[package]]
-category = "main"
-description = "Composable style cycles"
 name = "cycler"
+version = "0.10.0"
+description = "Composable style cycles"
+category = "main"
 optional = false
 python-versions = "*"
-version = "0.10.0"
 
 [package.dependencies]
 six = "*"
 
 [[package]]
-category = "main"
-description = ""
-name = "elog"
-optional = false
-python-versions = "*"
-version = "1.3.5"
-
-[package.source]
-reference = ""
-type = "url"
-url = "https://github.com/paulscherrerinstitute/py_elog/archive/master.zip"
-[[package]]
-category = "main"
-description = "Internationalized Domain Names in Applications (IDNA)"
 name = "idna"
+version = "2.10"
+description = "Internationalized Domain Names in Applications (IDNA)"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "2.9"
 
 [[package]]
-category = "dev"
-description = "Read metadata from Python packages"
-marker = "python_version < \"3.8\""
-name = "importlib-metadata"
-optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
-version = "1.6.0"
-
-[package.dependencies]
-zipp = ">=0.5"
-
-[package.extras]
-docs = ["sphinx", "rst.linker"]
-testing = ["packaging", "importlib-resources"]
-
-[[package]]
-category = "main"
-description = "A fast implementation of the Cassowary constraint solver"
 name = "kiwisolver"
+version = "1.3.1"
+description = "A fast implementation of the Cassowary constraint solver"
+category = "main"
 optional = false
 python-versions = ">=3.6"
-version = "1.2.0"
 
 [[package]]
-category = "main"
-description = "Python plotting package"
 name = "matplotlib"
+version = "3.3.2"
+description = "Python plotting package"
+category = "main"
 optional = false
 python-versions = ">=3.6"
-version = "3.2.1"
 
 [package.dependencies]
+certifi = ">=2020.06.20"
 cycler = ">=0.10"
 kiwisolver = ">=1.0.1"
-numpy = ">=1.11"
-pyparsing = ">=2.0.1,<2.0.4 || >2.0.4,<2.1.2 || >2.1.2,<2.1.6 || >2.1.6"
+numpy = ">=1.15"
+pillow = ">=6.2.0"
+pyparsing = ">=2.0.3,<2.0.4 || >2.0.4,<2.1.2 || >2.1.2,<2.1.6 || >2.1.6"
 python-dateutil = ">=2.1"
 
 [[package]]
-category = "dev"
-description = "More routines for operating on iterables, beyond itertools"
 name = "more-itertools"
+version = "8.6.0"
+description = "More routines for operating on iterables, beyond itertools"
+category = "dev"
 optional = false
 python-versions = ">=3.5"
-version = "8.2.0"
 
 [[package]]
-category = "main"
-description = "NumPy is the fundamental package for array computing with Python."
 name = "numpy"
+version = "1.19.4"
+description = "NumPy is the fundamental package for array computing with Python."
+category = "main"
 optional = false
-python-versions = ">=3.5"
-version = "1.18.4"
+python-versions = ">=3.6"
 
 [[package]]
-category = "dev"
-description = "Core utilities for Python packages"
 name = "packaging"
+version = "20.4"
+description = "Core utilities for Python packages"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "20.3"
 
 [package.dependencies]
 pyparsing = ">=2.0.2"
 six = "*"
 
 [[package]]
-category = "dev"
-description = "plugin and hook calling mechanisms for python"
+name = "pillow"
+version = "8.0.1"
+description = "Python Imaging Library (Fork)"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[[package]]
 name = "pluggy"
+version = "0.13.1"
+description = "plugin and hook calling mechanisms for python"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "0.13.1"
-
-[package.dependencies]
-[package.dependencies.importlib-metadata]
-python = "<3.8"
-version = ">=0.12"
 
 [package.extras]
 dev = ["pre-commit", "tox"]
 
 [[package]]
-category = "dev"
-description = "library with cross-python path, ini-parsing, io, code, log facilities"
 name = "py"
+version = "1.9.0"
+description = "library with cross-python path, ini-parsing, io, code, log facilities"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "1.8.1"
 
 [[package]]
-category = "main"
-description = "Python parsing module"
 name = "pyparsing"
+version = "2.4.7"
+description = "Python parsing module"
+category = "main"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
-version = "2.4.7"
 
 [[package]]
-category = "main"
-description = "Python bindings for the Qt cross platform application toolkit"
 name = "pyqt5"
+version = "5.15.1"
+description = "Python bindings for the Qt cross platform application toolkit"
+category = "main"
 optional = false
 python-versions = ">=3.5"
-version = "5.14.2"
 
 [package.dependencies]
-PyQt5-sip = ">=12.7,<13"
+PyQt5-sip = ">=12.8,<13"
 
 [[package]]
-category = "main"
-description = "The sip module support for PyQt5"
 name = "pyqt5-sip"
+version = "12.8.1"
+description = "The sip module support for PyQt5"
+category = "main"
 optional = false
 python-versions = ">=3.5"
-version = "12.7.2"
 
 [[package]]
-category = "dev"
-description = "pytest: simple powerful testing with Python"
 name = "pytest"
+version = "5.4.3"
+description = "pytest: simple powerful testing with Python"
+category = "dev"
 optional = false
 python-versions = ">=3.5"
-version = "5.4.1"
 
 [package.dependencies]
-atomicwrites = ">=1.0"
+atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
 attrs = ">=17.4.0"
-colorama = "*"
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
 more-itertools = ">=4.0.0"
 packaging = "*"
 pluggy = ">=0.12,<1.0"
 py = ">=1.5.0"
 wcwidth = "*"
 
-[package.dependencies.importlib-metadata]
-python = "<3.8"
-version = ">=0.12"
-
 [package.extras]
-checkqa-mypy = ["mypy (v0.761)"]
+checkqa-mypy = ["mypy (==v0.761)"]
 testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xmlschema"]
 
 [[package]]
-category = "main"
-description = "Extensions to the standard Python datetime module"
 name = "python-dateutil"
+version = "2.8.1"
+description = "Extensions to the standard Python datetime module"
+category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
-version = "2.8.1"
 
 [package.dependencies]
 six = ">=1.5"
 
 [[package]]
-category = "main"
-description = "Python HTTP for Humans."
 name = "requests"
+version = "2.24.0"
+description = "Python HTTP for Humans."
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-version = "2.23.0"
 
 [package.dependencies]
 certifi = ">=2017.4.17"
@@ -256,64 +227,52 @@ urllib3 = ">=1.21.1,<1.25.0 || >1.25.0,<1.25.1 || >1.25.1,<1.26"
 
 [package.extras]
 security = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)"]
-socks = ["PySocks (>=1.5.6,<1.5.7 || >1.5.7)", "win-inet-pton"]
+socks = ["PySocks (>=1.5.6,!=1.5.7)", "win-inet-pton"]
 
 [[package]]
-category = "main"
-description = "SciPy: Scientific Library for Python"
 name = "scipy"
+version = "1.5.3"
+description = "SciPy: Scientific Library for Python"
+category = "main"
 optional = false
-python-versions = ">=3.5"
-version = "1.4.1"
+python-versions = ">=3.6"
 
 [package.dependencies]
-numpy = ">=1.13.3"
+numpy = ">=1.14.5"
 
 [[package]]
-category = "main"
-description = "Python 2 and 3 compatibility utilities"
 name = "six"
+version = "1.15.0"
+description = "Python 2 and 3 compatibility utilities"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
-version = "1.14.0"
 
 [[package]]
-category = "main"
-description = "HTTP library with thread-safe connection pooling, file post, and more."
 name = "urllib3"
+version = "1.25.11"
+description = "HTTP library with thread-safe connection pooling, file post, and more."
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4"
-version = "1.25.9"
 
 [package.extras]
 brotli = ["brotlipy (>=0.6.0)"]
-secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "pyOpenSSL (>=0.14)", "ipaddress"]
-socks = ["PySocks (>=1.5.6,<1.5.7 || >1.5.7,<2.0)"]
+secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "ipaddress"]
+socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
 [[package]]
-category = "dev"
-description = "Measures number of Terminal column cells of wide-character codes"
 name = "wcwidth"
-optional = false
-python-versions = "*"
-version = "0.1.9"
-
-[[package]]
+version = "0.2.5"
+description = "Measures the displayed width of unicode strings in a terminal"
 category = "dev"
-description = "Backport of pathlib-compatible object wrapper for zip files"
-marker = "python_version < \"3.8\""
-name = "zipp"
 optional = false
-python-versions = ">=3.6"
-version = "3.1.0"
-
-[package.extras]
-docs = ["sphinx", "jaraco.packaging (>=3.2)", "rst.linker (>=1.9)"]
-testing = ["jaraco.itertools", "func-timeout"]
+python-versions = "*"
 
 [metadata]
-content-hash = "ab2440425657768cdf50a6b47e447622d9899d1704fd51c1f319514b3dddef0d"
-python-versions = "^3.6"
+lock-version = "1.1"
+python-versions = "^3.8"
+content-hash = "451da47b29bf3c71cec3e31f5f5f34516bce938905570d0665c0e101683ae5ee"
 
 [metadata.files]
 argparse = [
@@ -325,185 +284,241 @@ atomicwrites = [
     {file = "atomicwrites-1.4.0.tar.gz", hash = "sha256:ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a"},
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+    {file = "attrs-20.2.0-py2.py3-none-any.whl", hash = "sha256:fce7fc47dfc976152e82d53ff92fa0407700c21acd20886a13777a0d20e655dc"},
+    {file = "attrs-20.2.0.tar.gz", hash = "sha256:26b54ddbbb9ee1d34d5d3668dd37d6cf74990ab23c828c2888dccdceee395594"},
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 certifi = [
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+    {file = "certifi-2020.6.20-py2.py3-none-any.whl", hash = "sha256:8fc0819f1f30ba15bdb34cceffb9ef04d99f420f68eb75d901e9560b8749fc41"},
+    {file = "certifi-2020.6.20.tar.gz", hash = "sha256:5930595817496dd21bb8dc35dad090f1c2cd0adfaf21204bf6732ca5d8ee34d3"},
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 chardet = [
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-    {file = "colorama-0.4.3-py2.py3-none-any.whl", hash = "sha256:7d73d2a99753107a36ac6b455ee49046802e59d9d076ef8e47b61499fa29afff"},
-    {file = "colorama-0.4.3.tar.gz", hash = "sha256:e96da0d330793e2cb9485e9ddfd918d456036c7149416295932478192f4436a1"},
+    {file = "colorama-0.4.4-py2.py3-none-any.whl", hash = "sha256:9f47eda37229f68eee03b24b9748937c7dc3868f906e8ba69fbcbdd3bc5dc3e2"},
+    {file = "colorama-0.4.4.tar.gz", hash = "sha256:5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b"},
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diff --git a/pyproject.toml b/pyproject.toml
index 0680ba6..c0edaec 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "libhreels"
-version = "1.0.8"
+version = "1.1.1"
 description = "Handling, simulating, and plotting HREELS and Auger spectroscopy data"
 authors = ["Wolf Widdra <wolf.widdra@physik.uni-halle.de>"]
 include = ["*./libhreels/*"]
-- 
GitLab