diff --git a/README.md b/README.md index f56cc23..97d6484 100755 --- a/README.md +++ b/README.md @@ -32,7 +32,7 @@ Version 1.x documentation (deprecated): https://imctools.readthedocs.io Preferable way to install `imctools` is via official PyPI registry. Please define package version explicitly in order to avoid incompatibilities between v1.x and v2.x versions: ``` -pip install imctools==2.0.1 +pip install imctools==2.1.0 ``` In old IMC segmentation pipelines versions 1.x should be used! ``` diff --git a/docs/cli.html b/docs/cli.html index 879917c..0f2c305 100644 --- a/docs/cli.html +++ b/docs/cli.html @@ -3,7 +3,7 @@ - + imctools.cli API documentation @@ -268,7 +268,7 @@

Index

\ No newline at end of file diff --git a/docs/converters/exportacquisitioncsv.html b/docs/converters/exportacquisitioncsv.html index 75df0ad..577ee6d 100644 --- a/docs/converters/exportacquisitioncsv.html +++ b/docs/converters/exportacquisitioncsv.html @@ -3,7 +3,7 @@ - + imctools.converters.exportacquisitioncsv API documentation @@ -190,7 +190,7 @@

Index

\ No newline at end of file diff --git a/docs/converters/index.html b/docs/converters/index.html index 996bec1..0103604 100644 --- a/docs/converters/index.html +++ b/docs/converters/index.html @@ -3,7 +3,7 @@ - + imctools.converters API documentation @@ -93,7 +93,7 @@

Index

\ No newline at end of file diff --git a/docs/converters/mcdfolder2imcfolder.html b/docs/converters/mcdfolder2imcfolder.html index 845428d..a5dbd60 100644 --- a/docs/converters/mcdfolder2imcfolder.html +++ b/docs/converters/mcdfolder2imcfolder.html @@ -3,7 +3,7 @@ - + imctools.converters.mcdfolder2imcfolder API documentation @@ -98,11 +98,13 @@

Module imctools.converters.mcdfolder2imcfolder @@ -210,7 +212,7 @@

Index

\ No newline at end of file diff --git a/docs/converters/ome2analysis.html b/docs/converters/ome2analysis.html index 5f822b5..0a073c9 100644 --- a/docs/converters/ome2analysis.html +++ b/docs/converters/ome2analysis.html @@ -3,7 +3,7 @@ - + imctools.converters.ome2analysis API documentation @@ -495,7 +495,7 @@

Index

\ No newline at end of file diff --git a/docs/converters/ome2histocat.html b/docs/converters/ome2histocat.html index 29bd983..9e7d429 100644 --- a/docs/converters/ome2histocat.html +++ b/docs/converters/ome2histocat.html @@ -3,7 +3,7 @@ - + imctools.converters.ome2histocat API documentation @@ -369,7 +369,7 @@

Index

\ No newline at end of file diff --git a/docs/converters/v1tov2.html b/docs/converters/v1tov2.html index 2342420..3a079a3 100644 --- a/docs/converters/v1tov2.html +++ b/docs/converters/v1tov2.html @@ -3,7 +3,7 @@ - + imctools.converters.v1tov2 API documentation @@ -243,7 +243,7 @@

Index

\ No newline at end of file diff --git a/docs/data/acquisition.html b/docs/data/acquisition.html index 47f9776..29803f6 100644 --- a/docs/data/acquisition.html +++ b/docs/data/acquisition.html @@ -3,7 +3,7 @@ - + imctools.data.acquisition API documentation @@ -872,7 +872,7 @@

-

Generated by pdoc 0.8.4.

+

Generated by pdoc 0.8.5.

\ No newline at end of file diff --git a/docs/data/acquisitiondata.html b/docs/data/acquisitiondata.html index ad95e3b..f28a879 100644 --- a/docs/data/acquisitiondata.html +++ b/docs/data/acquisitiondata.html @@ -3,7 +3,7 @@ - + imctools.data.acquisitiondata API documentation @@ -900,7 +900,7 @@

-

Generated by pdoc 0.8.4.

+

Generated by pdoc 0.8.5.

\ No newline at end of file diff --git a/docs/data/channel.html b/docs/data/channel.html index abb5eeb..775c330 100644 --- a/docs/data/channel.html +++ b/docs/data/channel.html @@ -3,7 +3,7 @@ - + imctools.data.channel API documentation @@ -412,7 +412,7 @@

-

Generated by pdoc 0.8.4.

+

Generated by pdoc 0.8.5.

\ No newline at end of file diff --git a/docs/data/index.html b/docs/data/index.html index c1cc84d..6ce8726 100644 --- a/docs/data/index.html +++ b/docs/data/index.html @@ -3,7 +3,7 @@ - + imctools.data API documentation @@ -94,7 +94,7 @@

Index

\ No newline at end of file diff --git a/docs/data/panorama.html b/docs/data/panorama.html index 8237525..18d920d 100644 --- a/docs/data/panorama.html +++ b/docs/data/panorama.html @@ -3,7 +3,7 @@ - + imctools.data.panorama API documentation @@ -486,7 +486,7 @@

-

Generated by pdoc 0.8.4.

+

Generated by pdoc 0.8.5.

\ No newline at end of file diff --git a/docs/data/session.html b/docs/data/session.html index b1cd349..8a59ce3 100644 --- a/docs/data/session.html +++ b/docs/data/session.html @@ -3,7 +3,7 @@ - + imctools.data.session API documentation @@ -41,7 +41,7 @@

Module imctools.data.session

from imctools.data.channel import Channel, ChannelDict from imctools.data.panorama import Panorama, PanoramaDict from imctools.data.slide import Slide, SlideDict -from imctools.io.utils import META_CSV_SUFFIX +from imctools.io.utils import META_CSV_SUFFIX, sort_acquisition_channels if sys.version_info >= (3, 8): from typing import TypedDict # pylint: disable=no-name-in-module @@ -217,6 +217,9 @@

Module imctools.data.session

acquisition.channels[channel.id] = channel session.channels[channel.id] = channel + # Sort acquisitions channels by ORDER_NUMBER + sort_acquisition_channels(session) + return session @property @@ -236,7 +239,9 @@

Module imctools.data.session

import timeit tic = timeit.default_timer() - session = Session.load("/home/anton/Downloads/imc_from_mcd/20190919_FluidigmBrCa_SE_session.json") + session = Session.load( + "/home/anton/Downloads/imc_folder_v2/20170905_Fluidigmworkshopfinal_SEAJa/20170905_Fluidigmworkshopfinal_SEAJa_session.json" + ) print(timeit.default_timer() - tic) @@ -428,6 +433,9 @@

Parameters

acquisition.channels[channel.id] = channel session.channels[channel.id] = channel + # Sort acquisitions channels by ORDER_NUMBER + sort_acquisition_channels(session) + return session @property @@ -685,7 +693,7 @@

-

Generated by pdoc 0.8.4.

+

Generated by pdoc 0.8.5.

\ No newline at end of file diff --git a/docs/data/slide.html b/docs/data/slide.html index dfd99c9..9ffc98f 100644 --- a/docs/data/slide.html +++ b/docs/data/slide.html @@ -3,7 +3,7 @@ - + imctools.data.slide API documentation @@ -491,7 +491,7 @@

-

Generated by pdoc 0.8.4.

+

Generated by pdoc 0.8.5.

\ No newline at end of file diff --git a/docs/index.html b/docs/index.html index ce499b2..30002f0 100644 --- a/docs/index.html +++ b/docs/index.html @@ -3,7 +3,7 @@ - + imctools API documentation @@ -49,7 +49,7 @@

Prerequisites

Installation

Preferable way to install imctools is via official PyPI registry. Please define package version explicitly in order to avoid incompatibilities between v1.x and v2.x versions:

-
pip install imctools==2.0.1
+
pip install imctools==2.1.0
 

 
In old IMC segmentation pipelines versions 1.x should be used!

 
pip install imctools==1.0.8
@@ -57,7 +57,7 @@ 
Installation

 
Usage of version 2.x

 
imctools is often used from Jupyter as part of the pre-processing pipeline, mainly using the converters wrapper functions. Please check the following example as a template.

 
Further imctools can be directly used as a module:

-
from imctools.io.mcd.mcdparser import McdParser
+
from imctools.io.mcd.mcdparser import McdParser
 
 fn_mcd = "/home/vitoz/Data/varia/201708_instrument_comp/mcd/20170815_imccomp_zoidberg_conc5_acm1.mcd"
 
@@ -93,7 +93,7 @@ 
Usage of version 2.x

 parser.close()
 

 
Usage of previous version 1.x

-
import imctools.io.mcdparser as mcdparser
+
import imctools.io.mcdparser as mcdparser
 import imctools.io.txtparser as txtparser
 import imctools.io.ometiffparser as omeparser
 import imctools.io.mcdxmlparser as meta
@@ -140,7 +140,7 @@ 
Usage of previous version 1.x

 
 __author__ = """Vito Zanotelli, Anton Rau"""
 __email__ = "vito.zanotelli@uzh.ch, anton.rau@uzh.ch"
-__version__ = "2.0.1"

+__version__ = "2.1.0"

 
 
 

@@ -200,7 +200,7 @@ 
Index

 
 
 
 
 
\ No newline at end of file
diff --git a/docs/io/errors.html b/docs/io/errors.html
index 6a45207..47cab79 100644
--- a/docs/io/errors.html
+++ b/docs/io/errors.html
@@ -3,7 +3,7 @@
 
 
 
-
+
 imctools.io.errors API documentation
 
 
@@ -83,7 +83,7 @@ 

-
Generated by pdoc 0.8.4.

+
Generated by pdoc 0.8.5.

 
 
 
\ No newline at end of file
diff --git a/docs/io/imc/imcparser.html b/docs/io/imc/imcparser.html
index 425c10b..d42709c 100644
--- a/docs/io/imc/imcparser.html
+++ b/docs/io/imc/imcparser.html
@@ -3,7 +3,7 @@
 
 
 
-
+
 imctools.io.imc.imcparser API documentation
 
 
@@ -26,8 +26,7 @@ 
Module imctools.io.imc.imcparser

 
 Expand source code
 
-
import os
-from pathlib import Path
+
from pathlib import Path
 from typing import Union
 
 import tifffile
@@ -261,7 +260,7 @@ 

-
Generated by pdoc 0.8.4.

+
Generated by pdoc 0.8.5.

 
 
 
\ No newline at end of file
diff --git a/docs/io/imc/imcwriter.html b/docs/io/imc/imcwriter.html
index e4e7cdb..d99b2f3 100644
--- a/docs/io/imc/imcwriter.html
+++ b/docs/io/imc/imcwriter.html
@@ -3,7 +3,7 @@
 
 
 
-
+
 imctools.io.imc.imcwriter API documentation
 
 
@@ -392,7 +392,7 @@ 

-
Generated by pdoc 0.8.4.

+
Generated by pdoc 0.8.5.

 
 
 
\ No newline at end of file
diff --git a/docs/io/imc/index.html b/docs/io/imc/index.html
index 335c3e7..520cde5 100644
--- a/docs/io/imc/index.html
+++ b/docs/io/imc/index.html
@@ -3,7 +3,7 @@
 
 
 
-
+
 imctools.io.imc API documentation
 
 
@@ -64,7 +64,7 @@ 
Index

 
 
 
 
 
\ No newline at end of file
diff --git a/docs/io/index.html b/docs/io/index.html
index 7790220..8870d16 100644
--- a/docs/io/index.html
+++ b/docs/io/index.html
@@ -3,7 +3,7 @@
 
 
 
-
+
 imctools.io API documentation
 
 
@@ -84,7 +84,7 @@ 
Index

 
 
 
 
 
\ No newline at end of file
diff --git a/docs/io/mcd/constants.html b/docs/io/mcd/constants.html
index 0d0544c..8b12d2c 100644
--- a/docs/io/mcd/constants.html
+++ b/docs/io/mcd/constants.html
@@ -3,7 +3,7 @@
 
 
 
-
+
 imctools.io.mcd.constants API documentation
 
 
@@ -126,7 +126,7 @@ 
Index

 
 
 
 
 
\ No newline at end of file
diff --git a/docs/io/mcd/index.html b/docs/io/mcd/index.html
index 80a0f9c..6ebc6dc 100644
--- a/docs/io/mcd/index.html
+++ b/docs/io/mcd/index.html
@@ -3,7 +3,7 @@
 
 
 
-
+
 imctools.io.mcd API documentation
 
 
@@ -69,7 +69,7 @@ 
Index

 
 
 
 
 
\ No newline at end of file
diff --git a/docs/io/mcd/mcdparser.html b/docs/io/mcd/mcdparser.html
index 5ef5c03..62d5824 100644
--- a/docs/io/mcd/mcdparser.html
+++ b/docs/io/mcd/mcdparser.html
@@ -3,7 +3,7 @@
 
 
 
-
+
 imctools.io.mcd.mcdparser API documentation
 
 
@@ -323,9 +323,7 @@ 
Module imctools.io.mcd.mcdparser

     tic = timeit.default_timer()
 
     parser = McdParser(
-        Path(
-            "/home/anton/Documents/IMC Workshop 2019/Data/iMC_workshop_2019/20190919_FluidigmBrCa_SE/20190919_FluidigmBrCa_SE.mcd"
-        )
+        Path("/home/anton/Downloads/20170905_Fluidigmworkshopfinal_SEAJa/20170905_Fluidigmworkshopfinal_SEAJa.mcd")
     )
 
     print(timeit.default_timer() - tic)

@@ -954,7 +952,7 @@ 

-
Generated by pdoc 0.8.4.

+
Generated by pdoc 0.8.5.

 
 
 
\ No newline at end of file
diff --git a/docs/io/mcd/mcdxmlparser.html b/docs/io/mcd/mcdxmlparser.html
index 67d6929..f644bb3 100644
--- a/docs/io/mcd/mcdxmlparser.html
+++ b/docs/io/mcd/mcdxmlparser.html
@@ -3,7 +3,7 @@
 
 
 
-
+
 imctools.io.mcd.mcdxmlparser API documentation
 
 
@@ -37,6 +37,7 @@ 
Module imctools.io.mcd.mcdxmlparser

 import imctools.io.mcd.constants as const
 from imctools import __version__
 from imctools.data import Acquisition, Channel, Panorama, Session, Slide
+from imctools.io.utils import sort_acquisition_channels
 
 
 class McdXmlParser:
@@ -197,6 +198,9 @@ 
Module imctools.io.mcd.mcdxmlparser

                 channel.acquisition = ac
                 ac.channels[channel.id] = channel
 
+        # Sort acquisitions channels by ORDER_NUMBER
+        sort_acquisition_channels(session)
+
         self._session = session
 
     @property
@@ -400,6 +404,9 @@ 
Parameters

                 channel.acquisition = ac
                 ac.channels[channel.id] = channel
 
+        # Sort acquisitions channels by ORDER_NUMBER
+        sort_acquisition_channels(session)
+
         self._session = session
 
     @property
@@ -493,7 +500,7 @@ 

-
Generated by pdoc 0.8.4.

+
Generated by pdoc 0.8.5.

 
 
 
\ No newline at end of file
diff --git a/docs/io/ometiff/index.html b/docs/io/ometiff/index.html
index 4b5ef31..d647827 100644
--- a/docs/io/ometiff/index.html
+++ b/docs/io/ometiff/index.html
@@ -3,7 +3,7 @@
 
 
 
-
+
 imctools.io.ometiff API documentation
 
 
@@ -59,7 +59,7 @@ 
Index

 
 
 
 
 
\ No newline at end of file
diff --git a/docs/io/ometiff/ometiffparser.html b/docs/io/ometiff/ometiffparser.html
index c094b27..5da870d 100644
--- a/docs/io/ometiff/ometiffparser.html
+++ b/docs/io/ometiff/ometiffparser.html
@@ -3,7 +3,7 @@
 
 
 
-
+
 imctools.io.ometiff.ometiffparser API documentation
 
 
@@ -169,7 +169,7 @@ 
Module imctools.io.ometiff.ometiffparser

     tic = timeit.default_timer()
 
     with OmeTiffParser(
-        "/home/anton/Downloads/imc_folder/20170905_Fluidigmworkshopfinal_SEAJa/20170905_Fluidigmworkshopfinal_SEAJa_s0_a0_ac.ome.tiff"
+        "/home/anton/Downloads/imc_folder_v2/20170905_Fluidigmworkshopfinal_SEAJa/20170905_Fluidigmworkshopfinal_SEAJa_s0_a0_ac.ome.tiff"
     ) as parser:
         ac = parser.get_acquisition_data()
         pass
@@ -448,7 +448,7 @@ 

-
Generated by pdoc 0.8.4.

+
Generated by pdoc 0.8.5.

 
 
 
\ No newline at end of file
diff --git a/docs/io/txt/index.html b/docs/io/txt/index.html
index 48c4b58..f3f56ab 100644
--- a/docs/io/txt/index.html
+++ b/docs/io/txt/index.html
@@ -3,7 +3,7 @@
 
 
 
-
+
 imctools.io.txt API documentation
 
 
@@ -59,7 +59,7 @@ 
Index

 
 
 
 
 
\ No newline at end of file
diff --git a/docs/io/txt/txtparser.html b/docs/io/txt/txtparser.html
index 1db00d1..966d50a 100644
--- a/docs/io/txt/txtparser.html
+++ b/docs/io/txt/txtparser.html
@@ -3,7 +3,7 @@
 
 
 
-
+
 imctools.io.txt.txtparser API documentation
 
 
@@ -142,9 +142,9 @@ 
Module imctools.io.txt.txtparser

             dtype={c: np.float32 for c in header_cols[3:]},
         )
         data = df.values
-        names = [col for col in header_cols if col not in ("Start_push", "End_push", "Pushes_duration")]
-        channel_names = TxtParser._extract_channel_names(names)
-        channel_labels = TxtParser._extract_channel_labels(names)
+        channel_labels = [col for col in header_cols if col not in ("Start_push", "End_push", "Pushes_duration")]
+        channel_names = channel_labels[:]
+        channel_names[3:] = TxtParser._extract_channel_names(channel_names[3:])
         return data, channel_names, channel_labels
 
     @staticmethod
@@ -157,31 +157,31 @@ 
Module imctools.io.txt.txtparser

         names
             CSV file column names.
         """
-        r = re.compile(r"^.*\((.*?)\)[^(]*$")
-        r_number = re.compile(r"\d+")
-        result = []
-        for name in names:
-            n = (
-                r.sub(r"\g<1>", name.strip("\r").strip("\n").replace("(", "").replace(")", "").strip())
-                .rstrip("di")
-                .rstrip("Di")
-            )
-            metal_name = r_number.sub("", n)
-            metal_mass = n.replace(metal_name, "")
-            metal_mass = f"({metal_mass})" if metal_mass != "" else ""
-            result.append(f"{metal_name}{metal_mass}")
-        return result
+        # find which version it is
+        names = [n.strip("\r") for n in names]
+        names = [n.strip("\n") for n in names]
+        names = [n.strip() for n in names]
+        # string of sort asbsdf(mn123di)
+        if names[0].rfind(")") == (len(names[0]) - 1):
+            # get m123di
 
-    @staticmethod
-    def _extract_channel_labels(names: Sequence[str]):
-        """Returns channel labels in Fluidigm compatible format, i.e. Myelope_276((2669))Y89(Y89Di) or 80ArAr(ArAr80Di).
+            names = [n[(n.rfind("(") + 1) : (n.rfind(")"))] for n in names]
 
-        Parameters
-        ----------
-        names
-            CSV file column names.
-        """
-        return [name.strip("\r").strip("\n").strip() for name in names]
+        # string of sort aasbas_mn123
+        elif "_" in names[0]:
+            names = [n.split("_")[-1] for n in names]
+
+        # else do nothing
+        else:
+            return names
+
+        # else there is the bug where (123123di)
+        names = [n.rstrip("di") for n in names]
+        names = [n.rstrip("Di") for n in names]
+        if names[0][0].isdigit():
+            names = [n[(int(len(n) / 2)) :] for n in names]
+
+        return names
 
     def __enter__(self):
         return self
@@ -196,7 +196,7 @@ 
Module imctools.io.txt.txtparser

     tic = timeit.default_timer()
 
     with TxtParser(
-        "/home/anton/Documents/IMC Workshop 2019/Data/iMC_workshop_2019/20190919_FluidigmBrCa_SE/20190919_FluidigmBrCa_SE_BreastCa_1_1.txt"
+        "/home/anton/Downloads/20170905_Fluidigmworkshopfinal_SEAJa/Site1_0_ROI_1_upperleft_0.txt"
     ) as parser:
         ac = parser.get_acquisition_data()
         pass
@@ -326,9 +326,9 @@ 
Classes

             dtype={c: np.float32 for c in header_cols[3:]},
         )
         data = df.values
-        names = [col for col in header_cols if col not in ("Start_push", "End_push", "Pushes_duration")]
-        channel_names = TxtParser._extract_channel_names(names)
-        channel_labels = TxtParser._extract_channel_labels(names)
+        channel_labels = [col for col in header_cols if col not in ("Start_push", "End_push", "Pushes_duration")]
+        channel_names = channel_labels[:]
+        channel_names[3:] = TxtParser._extract_channel_names(channel_names[3:])
         return data, channel_names, channel_labels
 
     @staticmethod
@@ -341,31 +341,31 @@ 
Classes

         names
             CSV file column names.
         """
-        r = re.compile(r"^.*\((.*?)\)[^(]*$")
-        r_number = re.compile(r"\d+")
-        result = []
-        for name in names:
-            n = (
-                r.sub(r"\g<1>", name.strip("\r").strip("\n").replace("(", "").replace(")", "").strip())
-                .rstrip("di")
-                .rstrip("Di")
-            )
-            metal_name = r_number.sub("", n)
-            metal_mass = n.replace(metal_name, "")
-            metal_mass = f"({metal_mass})" if metal_mass != "" else ""
-            result.append(f"{metal_name}{metal_mass}")
-        return result
+        # find which version it is
+        names = [n.strip("\r") for n in names]
+        names = [n.strip("\n") for n in names]
+        names = [n.strip() for n in names]
+        # string of sort asbsdf(mn123di)
+        if names[0].rfind(")") == (len(names[0]) - 1):
+            # get m123di
 
-    @staticmethod
-    def _extract_channel_labels(names: Sequence[str]):
-        """Returns channel labels in Fluidigm compatible format, i.e. Myelope_276((2669))Y89(Y89Di) or 80ArAr(ArAr80Di).
+            names = [n[(n.rfind("(") + 1) : (n.rfind(")"))] for n in names]
 
-        Parameters
-        ----------
-        names
-            CSV file column names.
-        """
-        return [name.strip("\r").strip("\n").strip() for name in names]
+        # string of sort aasbas_mn123
+        elif "_" in names[0]:
+            names = [n.split("_")[-1] for n in names]
+
+        # else do nothing
+        else:
+            return names
+
+        # else there is the bug where (123123di)
+        names = [n.rstrip("di") for n in names]
+        names = [n.rstrip("Di") for n in names]
+        if names[0][0].isdigit():
+            names = [n[(int(len(n) / 2)) :] for n in names]
+
+        return names
 
     def __enter__(self):
         return self
@@ -483,7 +483,7 @@ 

-
Generated by pdoc 0.8.4.

+
Generated by pdoc 0.8.5.

 
 
 
\ No newline at end of file
diff --git a/docs/io/utils.html b/docs/io/utils.html
index 2f2a306..546a5c1 100644
--- a/docs/io/utils.html
+++ b/docs/io/utils.html
@@ -3,7 +3,7 @@
 
 
 
-
+
 imctools.io.utils API documentation
 
 
@@ -26,12 +26,17 @@ 
Module imctools.io.utils

 
 Expand source code
 
-
import xml.etree.ElementTree as ET
-from typing import Optional, Sequence
+
from __future__ import annotations
+
+import xml.etree.ElementTree as ET
+from typing import TYPE_CHECKING, Optional, Sequence
 
 import numpy as np
 import xtiff
 
+if TYPE_CHECKING:
+    from imctools.data import Session
+
 SESSION_JSON_SUFFIX = "_session.json"
 SCHEMA_XML_SUFFIX = "_schema.xml"
 OME_TIFF_SUFFIX = "_ac.ome.tiff"
@@ -127,7 +132,18 @@ 
Module imctools.io.utils

         ET.SubElement(original_metadata_element, "Key").text = "MCD-XML"
         ET.SubElement(original_metadata_element, "Value").text = xml_metadata.replace("\r\n", "")
 
-    return element_tree

+    return element_tree
+
+
+def sort_acquisition_channels(session: Session):
+    """Sort entries of acquisition channels dictionary by channel order number"""
+    for a in session.acquisitions.values():
+        ordered_dict = dict()
+        ac_channels = list(a.channels.values())
+        ac_channels.sort(key=lambda x: x.order_number)
+        for c in ac_channels:
+            ordered_dict[c.id] = c
+        a.channels = ordered_dict

 
 

 

@@ -138,7 +154,7 @@ 
Module imctools.io.utils

 
Functions

 

 

-def get_ome_xml(img: numpy.ndarray, image_name: Union[str, NoneType], channel_names: Union[Sequence[str], NoneType], big_endian: bool, pixel_size: Union[float, NoneType], pixel_depth: Union[float, NoneType], creator: Union[str, NoneType] = None, acquisition_date: Union[str, NoneType] = None, channel_fluors: Union[Sequence[str], NoneType] = None, xml_metadata: Union[str, NoneType] = None, **ome_xml_kwargs) ‑> xml.etree.ElementTree.ElementTree
+def get_ome_xml(img: np.ndarray, image_name: Optional[str], channel_names: Optional[Sequence[str]], big_endian: bool, pixel_size: Optional[float], pixel_depth: Optional[float], creator: Optional[str] = None, acquisition_date: Optional[str] = None, channel_fluors: Optional[Sequence[str]] = None, xml_metadata: Optional[str] = None, **ome_xml_kwargs) ‑> xml.etree.ElementTree.ElementTree
 

 

 
Helper function for xtiff library to get a proper OME-TIFF XML

@@ -194,7 +210,7 @@ 
Functions

 
 

 

-def reshape_long_2_cyx(data: numpy.memmap, is_sorted: bool = True, shape: Union[numpy.ndarray, NoneType] = None, channel_indices: Union[Sequence[int], NoneType] = None)
+def reshape_long_2_cyx(data: np.memmap, is_sorted: bool = True, shape: Optional[np.ndarray] = None, channel_indices: Optional[Sequence[int]] = None)
 

 

 
Reshape data from long format into cyx format (channels, y, x).

@@ -253,6 +269,26 @@ 
Parameters

         return NotImplemented

 
 
+

+def sort_acquisition_channels(session: Session)
+

+

+
Sort entries of acquisition channels dictionary by channel order number

+

+
+Expand source code
+
+
def sort_acquisition_channels(session: Session):
+    """Sort entries of acquisition channels dictionary by channel order number"""
+    for a in session.acquisitions.values():
+        ordered_dict = dict()
+        ac_channels = list(a.channels.values())
+        ac_channels.sort(key=lambda x: x.order_number)
+        for c in ac_channels:
+            ordered_dict[c.id] = c
+        a.channels = ordered_dict

+

+

 
 
 

@@ -273,13 +309,14 @@ 
Index

 
 
 
 
 
 
 
 
\ No newline at end of file
diff --git a/imctools/__init__.py b/imctools/__init__.py
index 8cfd016..05fb436 100644
--- a/imctools/__init__.py
+++ b/imctools/__init__.py
@@ -6,4 +6,4 @@
 
 __author__ = """Vito Zanotelli, Anton Rau"""
 __email__ = "vito.zanotelli@uzh.ch, anton.rau@uzh.ch"
-__version__ = "2.0.1"
+__version__ = "2.1.0"
diff --git a/imctools/converters/mcdfolder2imcfolder.py b/imctools/converters/mcdfolder2imcfolder.py
index c8b680b..a37d80e 100644
--- a/imctools/converters/mcdfolder2imcfolder.py
+++ b/imctools/converters/mcdfolder2imcfolder.py
@@ -70,11 +70,13 @@ def mcdfolder_to_imcfolder(input: Union[str, Path], output_folder: Union[str, Pa
     tic = timeit.default_timer()
 
     mcdfolder_to_imcfolder(
-        Path("/home/anton/Downloads/20170905_Fluidigmworkshopfinal_SEAJa.zip"),
+        # Path("/home/anton/Downloads/20170905_Fluidigmworkshopfinal_SEAJa.zip"),
+        "/home/anton/Downloads/20170905_Fluidigmworkshopfinal_SEAJa",
+        # "/home/anton/Documents/merrick/IMC/20200904_MS_XRF_epithelial_panel_4_titration.zip",
         # "/home/anton/Documents/IMC Workshop 2019/Data/iMC_workshop_2019/20190919_FluidigmBrCa_SE",
         # "/home/anton/Downloads/test",
         # "/home/anton/Data/ForAnton/20200123_IMMUcan_reproducibility_day1_sl1_cp_panel_1_1.06.zip",
-        Path("/home/anton/Downloads/imc_folder"),
+        Path("/home/anton/Downloads/imc_folder_v2"),
     )
 
     print(timeit.default_timer() - tic)
diff --git a/imctools/data/session.py b/imctools/data/session.py
index 2285f41..fd612af 100644
--- a/imctools/data/session.py
+++ b/imctools/data/session.py
@@ -13,7 +13,7 @@
 from imctools.data.channel import Channel, ChannelDict
 from imctools.data.panorama import Panorama, PanoramaDict
 from imctools.data.slide import Slide, SlideDict
-from imctools.io.utils import META_CSV_SUFFIX
+from imctools.io.utils import META_CSV_SUFFIX, sort_acquisition_channels
 
 if sys.version_info >= (3, 8):
     from typing import TypedDict  # pylint: disable=no-name-in-module
@@ -189,6 +189,9 @@ def _rebuild_object_tree(data: SessionDict):
             acquisition.channels[channel.id] = channel
             session.channels[channel.id] = channel
 
+        # Sort acquisitions channels by ORDER_NUMBER
+        sort_acquisition_channels(session)
+
         return session
 
     @property
@@ -208,5 +211,7 @@ def __repr__(self):
     import timeit
 
     tic = timeit.default_timer()
-    session = Session.load("/home/anton/Downloads/imc_from_mcd/20190919_FluidigmBrCa_SE_session.json")
+    session = Session.load(
+        "/home/anton/Downloads/imc_folder_v2/20170905_Fluidigmworkshopfinal_SEAJa/20170905_Fluidigmworkshopfinal_SEAJa_session.json"
+    )
     print(timeit.default_timer() - tic)
diff --git a/imctools/io/imc/imcparser.py b/imctools/io/imc/imcparser.py
index c1c2b9f..ff01e8f 100644
--- a/imctools/io/imc/imcparser.py
+++ b/imctools/io/imc/imcparser.py
@@ -1,4 +1,3 @@
-import os
 from pathlib import Path
 from typing import Union
 
diff --git a/imctools/io/mcd/mcdparser.py b/imctools/io/mcd/mcdparser.py
index f53f3ed..041ed0d 100644
--- a/imctools/io/mcd/mcdparser.py
+++ b/imctools/io/mcd/mcdparser.py
@@ -295,9 +295,7 @@ def __exit__(self, type, value, traceback):
     tic = timeit.default_timer()
 
     parser = McdParser(
-        Path(
-            "/home/anton/Documents/IMC Workshop 2019/Data/iMC_workshop_2019/20190919_FluidigmBrCa_SE/20190919_FluidigmBrCa_SE.mcd"
-        )
+        Path("/home/anton/Downloads/20170905_Fluidigmworkshopfinal_SEAJa/20170905_Fluidigmworkshopfinal_SEAJa.mcd")
     )
 
     print(timeit.default_timer() - tic)
diff --git a/imctools/io/mcd/mcdxmlparser.py b/imctools/io/mcd/mcdxmlparser.py
index 54e8de4..bff8638 100644
--- a/imctools/io/mcd/mcdxmlparser.py
+++ b/imctools/io/mcd/mcdxmlparser.py
@@ -9,6 +9,7 @@
 import imctools.io.mcd.constants as const
 from imctools import __version__
 from imctools.data import Acquisition, Channel, Panorama, Session, Slide
+from imctools.io.utils import sort_acquisition_channels
 
 
 class McdXmlParser:
@@ -169,6 +170,9 @@ def __init__(self, mcd_xml: str, source_path: str, process_namespaces=False):
                 channel.acquisition = ac
                 ac.channels[channel.id] = channel
 
+        # Sort acquisitions channels by ORDER_NUMBER
+        sort_acquisition_channels(session)
+
         self._session = session
 
     @property
diff --git a/imctools/io/ometiff/ometiffparser.py b/imctools/io/ometiff/ometiffparser.py
index 1038db0..d7a097d 100644
--- a/imctools/io/ometiff/ometiffparser.py
+++ b/imctools/io/ometiff/ometiffparser.py
@@ -141,7 +141,7 @@ def __exit__(self, type, value, traceback):
     tic = timeit.default_timer()
 
     with OmeTiffParser(
-        "/home/anton/Downloads/imc_folder/20170905_Fluidigmworkshopfinal_SEAJa/20170905_Fluidigmworkshopfinal_SEAJa_s0_a0_ac.ome.tiff"
+        "/home/anton/Downloads/imc_folder_v2/20170905_Fluidigmworkshopfinal_SEAJa/20170905_Fluidigmworkshopfinal_SEAJa_s0_a0_ac.ome.tiff"
     ) as parser:
         ac = parser.get_acquisition_data()
         pass
diff --git a/imctools/io/txt/txtparser.py b/imctools/io/txt/txtparser.py
index 1316d4e..779dba3 100644
--- a/imctools/io/txt/txtparser.py
+++ b/imctools/io/txt/txtparser.py
@@ -114,9 +114,9 @@ def _parse_csv(filepath: Path):
             dtype={c: np.float32 for c in header_cols[3:]},
         )
         data = df.values
-        names = [col for col in header_cols if col not in ("Start_push", "End_push", "Pushes_duration")]
-        channel_names = TxtParser._extract_channel_names(names)
-        channel_labels = TxtParser._extract_channel_labels(names)
+        channel_labels = [col for col in header_cols if col not in ("Start_push", "End_push", "Pushes_duration")]
+        channel_names = channel_labels[:]
+        channel_names[3:] = TxtParser._extract_channel_names(channel_names[3:])
         return data, channel_names, channel_labels
 
     @staticmethod
@@ -129,31 +129,31 @@ def _extract_channel_names(names: Sequence[str]):
         names
             CSV file column names.
         """
-        r = re.compile(r"^.*\((.*?)\)[^(]*$")
-        r_number = re.compile(r"\d+")
-        result = []
-        for name in names:
-            n = (
-                r.sub(r"\g<1>", name.strip("\r").strip("\n").replace("(", "").replace(")", "").strip())
-                .rstrip("di")
-                .rstrip("Di")
-            )
-            metal_name = r_number.sub("", n)
-            metal_mass = n.replace(metal_name, "")
-            metal_mass = f"({metal_mass})" if metal_mass != "" else ""
-            result.append(f"{metal_name}{metal_mass}")
-        return result
+        # find which version it is
+        names = [n.strip("\r") for n in names]
+        names = [n.strip("\n") for n in names]
+        names = [n.strip() for n in names]
+        # string of sort asbsdf(mn123di)
+        if names[0].rfind(")") == (len(names[0]) - 1):
+            # get m123di
 
-    @staticmethod
-    def _extract_channel_labels(names: Sequence[str]):
-        """Returns channel labels in Fluidigm compatible format, i.e. Myelope_276((2669))Y89(Y89Di) or 80ArAr(ArAr80Di).
+            names = [n[(n.rfind("(") + 1) : (n.rfind(")"))] for n in names]
 
-        Parameters
-        ----------
-        names
-            CSV file column names.
-        """
-        return [name.strip("\r").strip("\n").strip() for name in names]
+        # string of sort aasbas_mn123
+        elif "_" in names[0]:
+            names = [n.split("_")[-1] for n in names]
+
+        # else do nothing
+        else:
+            return names
+
+        # else there is the bug where (123123di)
+        names = [n.rstrip("di") for n in names]
+        names = [n.rstrip("Di") for n in names]
+        if names[0][0].isdigit():
+            names = [n[(int(len(n) / 2)) :] for n in names]
+
+        return names
 
     def __enter__(self):
         return self
@@ -168,7 +168,7 @@ def __exit__(self, type, value, traceback):
     tic = timeit.default_timer()
 
     with TxtParser(
-        "/home/anton/Documents/IMC Workshop 2019/Data/iMC_workshop_2019/20190919_FluidigmBrCa_SE/20190919_FluidigmBrCa_SE_BreastCa_1_1.txt"
+        "/home/anton/Downloads/20170905_Fluidigmworkshopfinal_SEAJa/Site1_0_ROI_1_upperleft_0.txt"
     ) as parser:
         ac = parser.get_acquisition_data()
         pass
diff --git a/imctools/io/utils.py b/imctools/io/utils.py
index 2755cce..3adc36f 100644
--- a/imctools/io/utils.py
+++ b/imctools/io/utils.py
@@ -1,9 +1,14 @@
+from __future__ import annotations
+
 import xml.etree.ElementTree as ET
-from typing import Optional, Sequence
+from typing import TYPE_CHECKING, Optional, Sequence
 
 import numpy as np
 import xtiff
 
+if TYPE_CHECKING:
+    from imctools.data import Session
+
 SESSION_JSON_SUFFIX = "_session.json"
 SCHEMA_XML_SUFFIX = "_schema.xml"
 OME_TIFF_SUFFIX = "_ac.ome.tiff"
@@ -100,3 +105,14 @@ def get_ome_xml(
         ET.SubElement(original_metadata_element, "Value").text = xml_metadata.replace("\r\n", "")
 
     return element_tree
+
+
+def sort_acquisition_channels(session: Session):
+    """Sort entries of acquisition channels dictionary by channel order number"""
+    for a in session.acquisitions.values():
+        ordered_dict = dict()
+        ac_channels = list(a.channels.values())
+        ac_channels.sort(key=lambda x: x.order_number)
+        for c in ac_channels:
+            ordered_dict[c.id] = c
+        a.channels = ordered_dict
diff --git a/poetry.lock b/poetry.lock
index cd4e21b..a43989c 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,69 +1,65 @@
 [[package]]
-category = "dev"
-description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 name = "appdirs"
+version = "1.4.4"
+description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+category = "dev"
 optional = false
 python-versions = "*"
-version = "1.4.4"
 
 [[package]]
-category = "dev"
-description = "An abstract syntax tree for Python with inference support."
 name = "astroid"
+version = "2.4.2"
+description = "An abstract syntax tree for Python with inference support."
+category = "dev"
 optional = false
 python-versions = ">=3.5"
-version = "2.4.2"
 
 [package.dependencies]
 lazy-object-proxy = ">=1.4.0,<1.5.0"
 six = ">=1.12,<2.0"
+typed-ast = {version = ">=1.4.0,<1.5", markers = "implementation_name == \"cpython\" and python_version < \"3.8\""}
 wrapt = ">=1.11,<2.0"
 
-[package.dependencies.typed-ast]
-python = "<3.8"
-version = ">=1.4.0,<1.5"
-
 [[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 = "dev"
-description = "Removes unused imports and unused variables"
 name = "autoflake"
+version = "1.4"
+description = "Removes unused imports and unused variables"
+category = "dev"
 optional = false
 python-versions = "*"
-version = "1.3.1"
 
 [package.dependencies]
 pyflakes = ">=1.1.0"
 
 [[package]]
-category = "dev"
-description = "The uncompromising code formatter."
 name = "black"
+version = "19.10b0"
+description = "The uncompromising code formatter."
+category = "dev"
 optional = false
 python-versions = ">=3.6"
-version = "19.10b0"
 
 [package.dependencies]
 appdirs = "*"
@@ -78,62 +74,58 @@ typed-ast = ">=1.4.0"
 d = ["aiohttp (>=3.3.2)", "aiohttp-cors"]
 
 [[package]]
-category = "dev"
-description = "Version-bump your software with a single command!"
 name = "bump2version"
+version = "1.0.1"
+description = "Version-bump your software with a single command!"
+category = "dev"
 optional = false
 python-versions = ">=3.5"
-version = "1.0.0"
 
 [[package]]
-category = "dev"
-description = "Composable command line interface toolkit"
 name = "click"
+version = "7.1.2"
+description = "Composable command line interface toolkit"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-version = "7.1.2"
 
 [[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 = "dev"
-description = "Code coverage measurement for Python"
 name = "coverage"
+version = "4.4.2"
+description = "Code coverage measurement for Python"
+category = "dev"
 optional = false
 python-versions = "*"
-version = "4.4.2"
 
 [[package]]
-category = "dev"
-description = "the modular source code checker: pep8 pyflakes and co"
 name = "flake8"
+version = "3.8.4"
+description = "the modular source code checker: pep8 pyflakes and co"
+category = "dev"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7"
-version = "3.8.3"
 
 [package.dependencies]
+importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
 mccabe = ">=0.6.0,<0.7.0"
 pycodestyle = ">=2.6.0a1,<2.7.0"
 pyflakes = ">=2.2.0,<2.3.0"
 
-[package.dependencies.importlib-metadata]
-python = "<3.8"
-version = "*"
-
 [[package]]
-category = "main"
-description = "Image transformation, compression, and decompression codecs"
 name = "imagecodecs"
+version = "2020.5.30"
+description = "Image transformation, compression, and decompression codecs"
+category = "main"
 optional = false
 python-versions = ">=3.6"
-version = "2020.5.30"
 
 [package.dependencies]
 numpy = ">=1.15.1"
@@ -142,13 +134,12 @@ numpy = ">=1.15.1"
 all = ["matplotlib (>=3.1)", "tifffile (>=2020.5.25)"]
 
 [[package]]
-category = "dev"
-description = "Read metadata from Python packages"
-marker = "python_version < \"3.8\""
 name = "importlib-metadata"
+version = "2.0.0"
+description = "Read metadata from Python packages"
+category = "dev"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
-version = "1.7.0"
 
 [package.dependencies]
 zipp = ">=0.5"
@@ -158,20 +149,20 @@ docs = ["sphinx", "rst.linker"]
 testing = ["packaging", "pep517", "importlib-resources (>=1.3)"]
 
 [[package]]
-category = "dev"
-description = "iniconfig: brain-dead simple config-ini parsing"
 name = "iniconfig"
+version = "1.1.1"
+description = "iniconfig: brain-dead simple config-ini parsing"
+category = "dev"
 optional = false
 python-versions = "*"
-version = "1.0.1"
 
 [[package]]
-category = "dev"
-description = "A Python utility / library to sort Python imports."
 name = "isort"
+version = "4.3.21"
+description = "A Python utility / library to sort Python imports."
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "4.3.21"
 
 [package.extras]
 pipfile = ["pipreqs", "requirementslib"]
@@ -180,20 +171,20 @@ requirements = ["pipreqs", "pip-api"]
 xdg_home = ["appdirs (>=1.4.0)"]
 
 [[package]]
-category = "dev"
-description = "A fast and thorough lazy object proxy."
 name = "lazy-object-proxy"
+version = "1.4.3"
+description = "A fast and thorough lazy object proxy."
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "1.4.3"
 
 [[package]]
-category = "dev"
-description = "A super-fast templating language that borrows the  best ideas from the existing templating languages."
 name = "mako"
+version = "1.1.3"
+description = "A super-fast templating language that borrows the  best ideas from the existing templating languages."
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "1.1.3"
 
 [package.dependencies]
 MarkupSafe = ">=0.9.2"
@@ -203,52 +194,42 @@ babel = ["babel"]
 lingua = ["lingua"]
 
 [[package]]
-category = "dev"
-description = "Python implementation of Markdown."
 name = "markdown"
+version = "3.3.1"
+description = "Python implementation of Markdown."
+category = "dev"
 optional = false
-python-versions = ">=3.5"
-version = "3.2.2"
+python-versions = ">=3.6"
 
 [package.dependencies]
-[package.dependencies.importlib-metadata]
-python = "<3.8"
-version = "*"
+importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
 
 [package.extras]
 testing = ["coverage", "pyyaml"]
 
 [[package]]
-category = "dev"
-description = "Safely add untrusted strings to HTML/XML markup."
 name = "markupsafe"
+version = "1.1.1"
+description = "Safely add untrusted strings to HTML/XML markup."
+category = "dev"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*"
-version = "1.1.1"
 
 [[package]]
-category = "dev"
-description = "McCabe checker, plugin for flake8"
 name = "mccabe"
-optional = false
-python-versions = "*"
 version = "0.6.1"
-
-[[package]]
+description = "McCabe checker, plugin for flake8"
 category = "dev"
-description = "More routines for operating on iterables, beyond itertools"
-name = "more-itertools"
 optional = false
-python-versions = ">=3.5"
-version = "8.4.0"
+python-versions = "*"
 
 [[package]]
-category = "dev"
-description = "Optional static typing for Python"
 name = "mypy"
+version = "0.790"
+description = "Optional static typing for Python"
+category = "dev"
 optional = false
 python-versions = ">=3.5"
-version = "0.782"
 
 [package.dependencies]
 mypy-extensions = ">=0.4.3,<0.5.0"
@@ -259,40 +240,40 @@ typing-extensions = ">=3.7.4"
 dmypy = ["psutil (>=4.0)"]
 
 [[package]]
-category = "dev"
-description = "Experimental type system extensions for programs checked with the mypy typechecker."
 name = "mypy-extensions"
+version = "0.4.3"
+description = "Experimental type system extensions for programs checked with the mypy typechecker."
+category = "dev"
 optional = false
 python-versions = "*"
-version = "0.4.3"
 
 [[package]]
-category = "main"
-description = "NumPy is the fundamental package for array computing with Python."
 name = "numpy"
+version = "1.19.2"
+description = "NumPy is the fundamental package for array computing with Python."
+category = "main"
 optional = false
 python-versions = ">=3.6"
-version = "1.19.1"
 
 [[package]]
-category = "main"
-description = "Core utilities for Python packages"
 name = "packaging"
+version = "20.4"
+description = "Core utilities for Python packages"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "20.4"
 
 [package.dependencies]
 pyparsing = ">=2.0.2"
 six = "*"
 
 [[package]]
-category = "main"
-description = "Powerful data structures for data analysis, time series, and statistics"
 name = "pandas"
+version = "1.1.3"
+description = "Powerful data structures for data analysis, time series, and statistics"
+category = "main"
 optional = false
 python-versions = ">=3.6.1"
-version = "1.1.0"
 
 [package.dependencies]
 numpy = ">=1.15.4"
@@ -303,122 +284,116 @@ pytz = ">=2017.2"
 test = ["pytest (>=4.0.2)", "pytest-xdist", "hypothesis (>=3.58)"]
 
 [[package]]
-category = "dev"
-description = "Utility library for gitignore style pattern matching of file paths."
 name = "pathspec"
+version = "0.8.0"
+description = "Utility library for gitignore style pattern matching of file paths."
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-version = "0.8.0"
 
 [[package]]
-category = "dev"
-description = "Auto-generate API documentation for Python projects."
 name = "pdoc3"
+version = "0.8.5"
+description = "Auto-generate API documentation for Python projects."
+category = "dev"
 optional = false
 python-versions = ">= 3.5"
-version = "0.8.4"
 
 [package.dependencies]
 mako = "*"
 markdown = ">=3.0"
 
 [[package]]
-category = "dev"
-description = "plugin and hook calling mechanisms for python"
 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"
+importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
 
 [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 = "1.9.0"
 
 [[package]]
-category = "dev"
-description = "Python style guide checker"
 name = "pycodestyle"
+version = "2.6.0"
+description = "Python style guide checker"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "2.6.0"
 
 [[package]]
-category = "dev"
-description = "passive checker of Python programs"
 name = "pyflakes"
+version = "2.2.0"
+description = "passive checker of Python programs"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "2.2.0"
 
 [[package]]
-category = "dev"
-description = "python code static checker"
 name = "pylint"
+version = "2.6.0"
+description = "python code static checker"
+category = "dev"
 optional = false
 python-versions = ">=3.5.*"
-version = "2.5.3"
 
 [package.dependencies]
 astroid = ">=2.4.0,<=2.5"
-colorama = "*"
-isort = ">=4.2.5,<5"
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
+isort = ">=4.2.5,<6"
 mccabe = ">=0.6,<0.7"
 toml = ">=0.7.1"
 
 [[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 = "dev"
-description = "pytest: simple powerful testing with Python"
 name = "pytest"
+version = "6.1.1"
+description = "pytest: simple powerful testing with Python"
+category = "dev"
 optional = false
 python-versions = ">=3.5"
-version = "6.0.1"
 
 [package.dependencies]
-atomicwrites = ">=1.0"
+atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
 attrs = ">=17.4.0"
-colorama = "*"
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
+importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
 iniconfig = "*"
-more-itertools = ">=4.0.0"
 packaging = "*"
 pluggy = ">=0.12,<1.0"
 py = ">=1.8.2"
 toml = "*"
 
-[package.dependencies.importlib-metadata]
-python = "<3.8"
-version = ">=0.12"
-
 [package.extras]
 checkqa_mypy = ["mypy (0.780)"]
 testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xmlschema"]
 
 [[package]]
-category = "dev"
-description = "Pytest plugin for measuring coverage."
 name = "pytest-cov"
+version = "2.10.1"
+description = "Pytest plugin for measuring coverage."
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-version = "2.10.0"
 
 [package.dependencies]
 coverage = ">=4.4"
@@ -428,131 +403,136 @@ pytest = ">=4.6"
 testing = ["fields", "hunter", "process-tests (2.0.2)", "six", "pytest-xdist", "virtualenv"]
 
 [[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 = "World timezone definitions, modern and historical"
 name = "pytz"
+version = "2020.1"
+description = "World timezone definitions, modern and historical"
+category = "main"
 optional = false
 python-versions = "*"
-version = "2020.1"
 
 [[package]]
-category = "dev"
-description = "Alternative regular expression module, to replace re."
 name = "regex"
+version = "2020.10.11"
+description = "Alternative regular expression module, to replace re."
+category = "dev"
 optional = false
 python-versions = "*"
-version = "2020.7.14"
 
 [[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 = "1.15.0"
 
 [[package]]
-category = "main"
-description = "Read and write TIFF(r) files"
 name = "tifffile"
+version = "2020.10.1"
+description = "Read and write TIFF(r) files"
+category = "main"
 optional = false
-python-versions = ">=3.6"
-version = "2020.8.13"
+python-versions = ">=3.7"
 
 [package.dependencies]
 numpy = ">=1.15.1"
 
 [package.extras]
-all = ["imagecodecs (>=2020.2.18)", "matplotlib (>=3.1)", "lxml"]
+all = ["imagecodecs (>=2020.5.30)", "matplotlib (>=3.2)", "lxml"]
 
 [[package]]
-category = "dev"
-description = "Python Library for Tom's Obvious, Minimal Language"
 name = "toml"
+version = "0.10.1"
+description = "Python Library for Tom's Obvious, Minimal Language"
+category = "dev"
 optional = false
 python-versions = "*"
-version = "0.10.1"
 
 [[package]]
-category = "dev"
-description = "a fork of Python 2 and 3 ast modules with type comment support"
 name = "typed-ast"
+version = "1.4.1"
+description = "a fork of Python 2 and 3 ast modules with type comment support"
+category = "dev"
 optional = false
 python-versions = "*"
-version = "1.4.1"
 
 [[package]]
-category = "main"
-description = "Backported and Experimental Type Hints for Python 3.5+"
 name = "typing-extensions"
+version = "3.7.4.3"
+description = "Backported and Experimental Type Hints for Python 3.5+"
+category = "main"
 optional = false
 python-versions = "*"
-version = "3.7.4.2"
 
 [[package]]
-category = "dev"
-description = "Find dead code"
 name = "vulture"
+version = "2.1"
+description = "Find dead code"
+category = "dev"
 optional = false
 python-versions = ">=3.6"
-version = "2.0"
+
+[package.dependencies]
+toml = "*"
 
 [[package]]
-category = "dev"
-description = "Module for decorators, wrappers and monkey patching."
 name = "wrapt"
+version = "1.12.1"
+description = "Module for decorators, wrappers and monkey patching."
+category = "dev"
 optional = false
 python-versions = "*"
-version = "1.12.1"
 
 [[package]]
-category = "main"
-description = "Makes working with XML feel like you are working with JSON"
 name = "xmltodict"
+version = "0.12.0"
+description = "Makes working with XML feel like you are working with JSON"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-version = "0.12.0"
 
 [[package]]
-category = "main"
-description = "A tiny Python 3 library for writing multi-channel TIFF stacks"
 name = "xtiff"
+version = "0.6.2"
+description = "A tiny Python 3 library for writing multi-channel TIFF stacks"
+category = "main"
 optional = false
 python-versions = ">=3.7"
-version = "0.6.1"
 
 [package.dependencies]
 numpy = "*"
-tifffile = "*"
+tifffile = ">=2020.6.3,<2020.7.17 || >2020.7.17"
+
+[package.extras]
+xtiff_support = ["xtiff"]
 
 [[package]]
-category = "dev"
-description = "Backport of pathlib-compatible object wrapper for zip files"
-marker = "python_version < \"3.8\""
 name = "zipp"
+version = "3.3.0"
+description = "Backport of pathlib-compatible object wrapper for zip files"
+category = "dev"
 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"]
+testing = ["pytest (>=3.5,<3.7.3 || >3.7.3)", "pytest-checkdocs (>=1.2.3)", "pytest-flake8", "pytest-cov", "jaraco.test (>=3.2.0)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy"]
 
 [metadata]
-content-hash = "dd6c9c2164e589708fde98ff53a32acb63350ba74d28a83267c3a771493bd402"
-lock-version = "1.0"
+lock-version = "1.1"
 python-versions = ">=3.7"
+content-hash = "e15e7e6c724344f684bb20df7909e85291985b5b1f51633c2279fa0a44ee27db"
 
 [metadata.files]
 appdirs = [
@@ -568,27 +548,26 @@ atomicwrites = [
     {file = "atomicwrites-1.4.0.tar.gz", hash = "sha256:ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a"},
 ]
 attrs = [
-    {file = "attrs-19.3.0-py2.py3-none-any.whl", hash = "sha256:08a96c641c3a74e44eb59afb61a24f2cb9f4d7188748e76ba4bb5edfa3cb7d1c"},
-    {file = "attrs-19.3.0.tar.gz", hash = "sha256:f7b7ce16570fe9965acd6d30101a28f62fb4a7f9e926b3bbc9b61f8b04247e72"},
+    {file = "attrs-20.2.0-py2.py3-none-any.whl", hash = "sha256:fce7fc47dfc976152e82d53ff92fa0407700c21acd20886a13777a0d20e655dc"},
+    {file = "attrs-20.2.0.tar.gz", hash = "sha256:26b54ddbbb9ee1d34d5d3668dd37d6cf74990ab23c828c2888dccdceee395594"},
 ]
 autoflake = [
-    {file = "autoflake-1.3.1.tar.gz", hash = "sha256:680cb9dade101ed647488238ccb8b8bfb4369b53d58ba2c8cdf7d5d54e01f95b"},
+    {file = "autoflake-1.4.tar.gz", hash = "sha256:61a353012cff6ab94ca062823d1fb2f692c4acda51c76ff83a8d77915fba51ea"},
 ]
 black = [
     {file = "black-19.10b0-py36-none-any.whl", hash = "sha256:1b30e59be925fafc1ee4565e5e08abef6b03fe455102883820fe5ee2e4734e0b"},
     {file = "black-19.10b0.tar.gz", hash = "sha256:c2edb73a08e9e0e6f65a0e6af18b059b8b1cdd5bef997d7a0b181df93dc81539"},
 ]
 bump2version = [
-    {file = "bump2version-1.0.0-py2.py3-none-any.whl", hash = "sha256:477f0e18a0d58e50bb3dbc9af7fcda464fd0ebfc7a6151d8888602d7153171a0"},
-    {file = "bump2version-1.0.0.tar.gz", hash = "sha256:cd4f3a231305e405ed8944d8ff35bd742d9bc740ad62f483bd0ca21ce7131984"},
+    {file = "bump2version-1.0.1-py2.py3-none-any.whl", hash = "sha256:37f927ea17cde7ae2d7baf832f8e80ce3777624554a653006c9144f8017fe410"},
+    {file = "bump2version-1.0.1.tar.gz", hash = "sha256:762cb2bfad61f4ec8e2bdf452c7c267416f8c70dd9ecb1653fd0bbb01fa936e6"},
 ]
 click = [
     {file = "click-7.1.2-py2.py3-none-any.whl", hash = "sha256:dacca89f4bfadd5de3d7489b7c8a566eee0d3676333fbb50030263894c38c0dc"},
     {file = "click-7.1.2.tar.gz", hash = "sha256:d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a"},
 ]
 colorama = [
-    {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"},
 ]
 coverage = [
     {file = "coverage-4.4.2-cp26-cp26m-macosx_10_10_x86_64.whl", hash = "sha256:d1ee76f560c3c3e8faada866a07a32485445e16ed2206ac8378bd90dadffb9f0"},
@@ -633,8 +612,8 @@ coverage = [
     {file = "coverage-4.4.2.win32-py3.6.exe", hash = "sha256:f98b461cb59f117887aa634a66022c0bd394278245ed51189f63a036516e32de"},
 ]
 flake8 = [
-    {file = "flake8-3.8.3-py2.py3-none-any.whl", hash = "sha256:15e351d19611c887e482fb960eae4d44845013cc142d42896e9862f775d8cf5c"},
-    {file = "flake8-3.8.3.tar.gz", hash = "sha256:f04b9fcbac03b0a3e58c0ab3a0ecc462e023a9faf046d57794184028123aa208"},
+    {file = "flake8-3.8.4-py2.py3-none-any.whl", hash = "sha256:749dbbd6bfd0cf1318af27bf97a14e28e5ff548ef8e5b1566ccfb25a11e7c839"},
+    {file = "flake8-3.8.4.tar.gz", hash = "sha256:aadae8761ec651813c24be05c6f7b4680857ef6afaae4651a4eccaef97ce6c3b"},
 ]
 imagecodecs = [
     {file = "imagecodecs-2020.5.30-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:110318270910b3b62941da60fed009dd669434d6344675c48d25df5207cdafa1"},
@@ -660,12 +639,11 @@ imagecodecs = [
     {file = "imagecodecs-2020.5.30.tar.gz", hash = "sha256:c8c776922d3a60824d8d3d31ba674a250d1b4d429e81349b5c88c34d4353ddb5"},
 ]
 importlib-metadata = [
-    {file = "importlib_metadata-1.7.0-py2.py3-none-any.whl", hash = "sha256:dc15b2969b4ce36305c51eebe62d418ac7791e9a157911d58bfb1f9ccd8e2070"},
-    {file = "importlib_metadata-1.7.0.tar.gz", hash = "sha256:90bb658cdbbf6d1735b6341ce708fc7024a3e14e99ffdc5783edea9f9b077f83"},
+    {file = "importlib_metadata-2.0.0-py2.py3-none-any.whl", hash = "sha256:cefa1a2f919b866c5beb7c9f7b0ebb4061f30a8a9bf16d609b000e2dfaceb9c3"},
+    {file = "importlib_metadata-2.0.0.tar.gz", hash = "sha256:77a540690e24b0305878c37ffd421785a6f7e53c8b5720d211b211de8d0e95da"},
 ]
 iniconfig = [
-    {file = "iniconfig-1.0.1-py3-none-any.whl", hash = "sha256:80cf40c597eb564e86346103f609d74efce0f6b4d4f30ec8ce9e2c26411ba437"},
-    {file = "iniconfig-1.0.1.tar.gz", hash = "sha256:e5f92f89355a67de0595932a6c6c02ab4afddc6fcdc0bfc5becd0d60884d3f69"},
+    {file = "iniconfig-1.1.1.tar.gz", hash = "sha256:bc3af051d7d14b2ee5ef9969666def0cd1a000e121eaea580d4a313df4b37f32"},
 ]
 isort = [
     {file = "isort-4.3.21-py2.py3-none-any.whl", hash = "sha256:6e811fcb295968434526407adb8796944f1988c5b65e8139058f2014cbe100fd"},
@@ -699,8 +677,8 @@ mako = [
     {file = "Mako-1.1.3.tar.gz", hash = "sha256:8195c8c1400ceb53496064314c6736719c6f25e7479cd24c77be3d9361cddc27"},
 ]
 markdown = [
-    {file = "Markdown-3.2.2-py3-none-any.whl", hash = "sha256:c467cd6233885534bf0fe96e62e3cf46cfc1605112356c4f9981512b8174de59"},
-    {file = "Markdown-3.2.2.tar.gz", hash = "sha256:1fafe3f1ecabfb514a5285fca634a53c1b32a81cb0feb154264d55bf2ff22c17"},
+    {file = "Markdown-3.3.1-py3-none-any.whl", hash = "sha256:10db1204a6c4aff7c7cf3cf25cc02761703baea54b6fb5e2b9ce2c186d81116f"},
+    {file = "Markdown-3.3.1.tar.gz", hash = "sha256:c3ce9ebb035c078cac0f2036068d054e7dc34354eeecc49c173c33c96b124af6"},
 ]
 markupsafe = [
     {file = "MarkupSafe-1.1.1-cp27-cp27m-macosx_10_6_intel.whl", hash = "sha256:09027a7803a62ca78792ad89403b1b7a73a01c8cb65909cd876f7fcebd79b161"},
@@ -741,86 +719,82 @@ mccabe = [
     {file = "mccabe-0.6.1-py2.py3-none-any.whl", hash = "sha256:ab8a6258860da4b6677da4bd2fe5dc2c659cff31b3ee4f7f5d64e79735b80d42"},
     {file = "mccabe-0.6.1.tar.gz", hash = "sha256:dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f"},
 ]
-more-itertools = [
-    {file = "more-itertools-8.4.0.tar.gz", hash = "sha256:68c70cc7167bdf5c7c9d8f6954a7837089c6a36bf565383919bb595efb8a17e5"},
-    {file = "more_itertools-8.4.0-py3-none-any.whl", hash = "sha256:b78134b2063dd214000685165d81c154522c3ee0a1c0d4d113c80361c234c5a2"},
-]
 mypy = [
-    {file = "mypy-0.782-cp35-cp35m-macosx_10_6_x86_64.whl", hash = "sha256:2c6cde8aa3426c1682d35190b59b71f661237d74b053822ea3d748e2c9578a7c"},
-    {file = "mypy-0.782-cp35-cp35m-manylinux1_x86_64.whl", hash = "sha256:9c7a9a7ceb2871ba4bac1cf7217a7dd9ccd44c27c2950edbc6dc08530f32ad4e"},
-    {file = "mypy-0.782-cp35-cp35m-win_amd64.whl", hash = "sha256:c05b9e4fb1d8a41d41dec8786c94f3b95d3c5f528298d769eb8e73d293abc48d"},
-    {file = "mypy-0.782-cp36-cp36m-macosx_10_6_x86_64.whl", hash = "sha256:6731603dfe0ce4352c555c6284c6db0dc935b685e9ce2e4cf220abe1e14386fd"},
-    {file = "mypy-0.782-cp36-cp36m-manylinux1_x86_64.whl", hash = "sha256:f05644db6779387ccdb468cc47a44b4356fc2ffa9287135d05b70a98dc83b89a"},
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@@ -921,13 +901,13 @@ typed-ast = [
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@@ -937,9 +917,9 @@ xmltodict = [
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diff --git a/pyproject.toml b/pyproject.toml
index ad1c847..0a556e4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "poetry.masonry.api"
 
 [tool.poetry]
 name = "imctools"
-version = "2.0.1"
+version = "2.1.0"
 description = "Tools to handle Fluidigm IMC data"
 license = "MIT"
 authors = ["Vito Zanotelli ", "Anton Rau "]
@@ -29,7 +29,7 @@ packaging = "*"
 pandas = "^1.0"
 typing_extensions = ">=3.7.4.2"
 xmltodict = ">=0.12.0"
-xtiff = ">=0.6.1"
+xtiff = ">=0.6.2"
 
 [tool.poetry.dev-dependencies]
 autoflake = "^1.3.1"
diff --git a/setup.cfg b/setup.cfg
index 2edb76f..479143b 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.0.1
+current_version = 2.1.0
 commit = False
 tag = False
 
diff --git a/tests/test_mcdparser.py b/tests/test_mcdparser.py
index 44e13f8..eb19cc7 100644
--- a/tests/test_mcdparser.py
+++ b/tests/test_mcdparser.py
@@ -7,7 +7,7 @@
 
 sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
 
-TEST_DATA_URL = 'https://dl.dropboxusercontent.com/s/g1zs5jy49804133/testdata_v2.zip'
+TEST_DATA_URL = 'https://dl.dropboxusercontent.com/s/d8jk9zpi6rzcmsf/testdata_v2.1.zip'
 TEST_DATA_FOLDER = os.path.join(os.path.dirname(__file__), 'testdata')
 TEST_ACQUISITIONS = os.path.join(TEST_DATA_FOLDER, 'acquisitions')
 TEST_RESULTS = os.path.join(TEST_DATA_FOLDER, 'test_results')
@@ -41,7 +41,7 @@ def test_parser(self):
     def _get_test_cases():
         if not os.path.exists(TEST_DATA_FOLDER):
             os.makedirs(TEST_DATA_FOLDER)
-        zip_file = os.path.join(TEST_DATA_FOLDER, 'testdata_v2.zip')
+        zip_file = os.path.join(TEST_DATA_FOLDER, 'testdata_v2.1.zip')
         if not os.path.isfile(zip_file):
             urlretrieve(TEST_DATA_URL, zip_file)