- First commit

ndbioimage/readers/seqread.py

@@ -0,0 +1,85 @@
+from ndbioimage import Imread, XmlData
+import os
+import tifffile
+import yaml
+import json
+import re
+
+
+class Reader(Imread):
+    priority = 10
+
+    @staticmethod
+    def _can_open(path):
+        return isinstance(path, str) and os.path.splitext(path)[1] == ''
+
+    def __metadata__(self):
+        filelist = sorted([file for file in os.listdir(self.path) if re.search(r'^img_\d{3,}.*\d{3,}.*\.tif$', file)])
+
+        try:
+            with tifffile.TiffFile(os.path.join(self.path, filelist[0])) as tif:
+                self.metadata = XmlData({key: yaml.safe_load(value)
+                                         for key, value in tif.pages[0].tags[50839].value.items()})
+        except Exception:  # fallback
+            with open(os.path.join(self.path, 'metadata.txt'), 'r') as metadatafile:
+                self.metadata = XmlData(json.loads(metadatafile.read()))
+
+        # compare channel names from metadata with filenames
+        cnamelist = self.metadata.search('ChNames')
+        cnamelist = [c for c in cnamelist if any([c in f for f in filelist])]
+
+        self.filedict = {}
+        maxc = 0
+        maxz = 0
+        maxt = 0
+        for file in filelist:
+            T = re.search(r'(?<=img_)\d{3,}', file)
+            Z = re.search(r'\d{3,}(?=\.tif$)', file)
+            C = file[T.end() + 1:Z.start() - 1]
+            t = int(T.group(0))
+            z = int(Z.group(0))
+            if C in cnamelist:
+                c = cnamelist.index(C)
+            else:
+                c = len(cnamelist)
+                cnamelist.append(C)
+
+            self.filedict[(c, z, t)] = file
+            if c > maxc:
+                maxc = c
+            if z > maxz:
+                maxz = z
+            if t > maxt:
+                maxt = t
+        self.cnamelist = [str(cname) for cname in cnamelist]
+
+        X = self.metadata.search('Width')[0]
+        Y = self.metadata.search('Height')[0]
+        self.shape = (int(X), int(Y), maxc + 1, maxz + 1, maxt + 1)
+
+        self.pxsize = self.metadata.re_search(r'(?i)pixelsize_?um', 0)[0]
+        if self.zstack:
+            self.deltaz = self.metadata.re_search(r'(?i)z-step_?um', 0)[0]
+        if self.timeseries:
+            self.settimeinterval = self.metadata.re_search(r'(?i)interval_?ms', 0)[0] / 1000
+        if 'Hamamatsu' in self.metadata.search('Core-Camera', '')[0]:
+            self.pxsizecam = 6.5
+        self.title = self.metadata.search('Prefix')[0]
+        self.acquisitiondate = self.metadata.search('Time')[0]
+        self.exposuretime = [i / 1000 for i in self.metadata.search('Exposure-ms')]
+        self.objective = self.metadata.search('ZeissObjectiveTurret-Label')[0]
+        self.optovar = []
+        for o in self.metadata.search('ZeissOptovar-Label'):
+            a = re.search(r'\d?\d*[,.]?\d+(?=x$)', o)
+            if hasattr(a, 'group'):
+                self.optovar.append(float(a.group(0).replace(',', '.')))
+        if self.pxsize == 0:
+            self.magnification = int(re.findall(r'(\d+)x', self.objective)[0]) * self.optovar[0]
+            self.pxsize = self.pxsizecam / self.magnification
+        else:
+            self.magnification = self.pxsizecam / self.pxsize
+        self.pcf = self.shape[2] * self.metadata.re_search(r'(?i)conversion\sfactor\scoeff', 1)
+        self.filter = self.metadata.search('ZeissReflectorTurret-Label', self.filter)[0]
+
+    def __frame__(self, c=0, z=0, t=0):
+        return tifffile.imread(os.path.join(self.path, self.filedict[(c, z, t)]))