bump versions and refactor for tifffile

RI-imaging · May 28, 2020 · f1d055b · f1d055b
1 parent e0e3701
commit f1d055b
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Showing 5 changed files with 31 additions and 20 deletions.
diff --git a/CHANGELOG b/CHANGELOG
@@ -1,3 +1,7 @@
+0.10.5
+ - setup: bump qpimage from 0.6.1 to 0.6.2
+ - setup: change dependency of scikit-image to tifffile 2020.5.25
+ - ref: make code work with latest version of tifffile
 0.10.4
  - setup: bump qpimage from 0.5.0 to 0.6.1
 0.10.3

diff --git a/qpformat/file_formats/single_tif_holo.py b/qpformat/file_formats/single_tif_holo.py
@@ -4,7 +4,7 @@
 
 import numpy as np
 import qpimage
-from skimage.external import tifffile
+import tifffile
 
 from .dataset import SingleData
 
@@ -59,9 +59,10 @@ def verify(path):
         valid = False
         try:
             tf = SingleTifHolo._get_tif(path)
-        except (ValueError, IsADirectoryError):
+        except (ValueError, IsADirectoryError, KeyError,
+                tifffile.tifffile.TiffFileError):
             pass
         else:
-            if len(tf) == 1:
+            if len(tf.pages) == 1:
                 valid = True
         return valid
diff --git a/qpformat/file_formats/single_tif_phasics.py b/qpformat/file_formats/single_tif_phasics.py
@@ -6,14 +6,19 @@
 
 import numpy as np
 import qpimage
-from skimage.external import tifffile
+import tifffile
 
 from .dataset import SingleData
 
 
 # baseline clamp intensity normalization for phasics tif files
 INTENSITY_BASELINE_CLAMP = 150
 
+# https://www.loc.gov/preservation/digital/formats/content/tiff_tags.shtml
+TIFF_TAGS = {
+    "MaxSampleValue": 281,
+    }
+
 
 class LoadTifPhasicsError(BaseException):
     pass
@@ -52,7 +57,7 @@ def __init__(self, path, meta_data={}, *args, **kwargs):
     @staticmethod
     def _get_meta_data(path, section, name):
         with SingleTifPhasics._get_tif(path) as tf:
-            meta = tf.pages[0].tags["61238"].as_str()
+            meta = tf.pages[0].tags[61238].value
 
         meta = meta.strip("'b")
         meta = meta.replace("\\n", "\n")
@@ -123,7 +128,7 @@ def get_qpimage_raw(self, idx=0):
             inttags = tf.pages[0].tags
             imin = inttags["61243"].value
             imax = inttags["61242"].value
-            isamp = inttags["max_sample_value"].value
+            isamp = inttags[TIFF_TAGS["MaxSampleValue"]].value
             blc = INTENSITY_BASELINE_CLAMP
             inten = tf.pages[0].asarray() * (imax - imin) / isamp + imin - blc
             inten[inten < 0] = 0
@@ -153,7 +158,7 @@ def get_qpimage_raw(self, idx=0):
             phatags = tf.pages[phaid].tags
             pmin = phatags["61243"].value
             pmax = phatags["61242"].value
-            psamp = phatags["max_sample_value"].value
+            psamp = phatags[TIFF_TAGS["MaxSampleValue"]].value
             if psamp == 0 or pmin == pmax:
                 # no phase data
                 pha = np.zeros_like(inten)
@@ -183,17 +188,18 @@ def verify(path):
         valid = False
         try:
             tf = SingleTifPhasics._get_tif(path)
-        except (ValueError, IsADirectoryError):
+        except (ValueError, IsADirectoryError, KeyError,
+                tifffile.tifffile.TiffFileError):
             pass
         else:
-            if (len(tf) == 3 and
-                "61243" in tf.pages[0].tags and
-                "61242" in tf.pages[0].tags and
-                "61238" in tf.pages[0].tags and
-                "61243" in tf.pages[1].tags and
-                "61242" in tf.pages[1].tags and
-                "max_sample_value" in tf.pages[0].tags and
-                (tf.pages[0].tags["61242"].value !=
-                 tf.pages[1].tags["61242"].value)):
+            if (len(tf.pages) == 3 and
+                61243 in tf.pages[0].tags and
+                61242 in tf.pages[0].tags and
+                61238 in tf.pages[0].tags and
+                61243 in tf.pages[1].tags and
+                61242 in tf.pages[1].tags and
+                TIFF_TAGS["MaxSampleValue"] in tf.pages[0].tags and
+                (tf.pages[0].tags[61242].value !=
+                 tf.pages[1].tags[61242].value)):
                 valid = True
         return valid
diff --git a/setup.py b/setup.py
@@ -26,8 +26,8 @@
     install_requires=["h5py>=2.7.0",
                       "nrefocus>=0.1.5",
                       "numpy>=1.12.0",
-                      "qpimage>=0.6.1",
-                      "scikit-image>=0.11.0",
+                      "qpimage>=0.6.2",
+                      "tifffile>=2020.5.25",
                       "scipy>=0.18.0",
                       ],
     setup_requires=['pytest-runner'],

diff --git a/tests/test_series_hdf5_hyperspy.py b/tests/test_series_hdf5_hyperspy.py
@@ -5,7 +5,7 @@
 import warnings
 
 import h5py
-from skimage.external import tifffile
+import tifffile
 
 import qpformat
 from qpformat.file_formats import WrongFileFormatError