Change dye_names from array of string to string with CSV text.

Closes #2.
Photon-HDF5 · Jun 23, 2015 · 8421904 · 8421904
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commit 8421904
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Showing 4 changed files with 21 additions and 21 deletions.
diff --git a/notebooks/Convert ns-ALEX Becker-Hickl files to Photon-HDF5.ipynb b/notebooks/Convert ns-ALEX Becker-Hickl files to Photon-HDF5.ipynb
@@ -137,7 +137,7 @@
    "source": [
     "description = 'A demonstrative smFRET-nsALEX measurement.'\n",
     "sample_name = '50-50 mixture of two FRET samples'\n",
-    "dye_names = ['ATTO550', 'ATTO647N']\n",
+    "dye_names = 'ATTO550, ATTO647N'\n",
     "buffer_name = 'TE50'"
    ]
   },
@@ -289,9 +289,9 @@
     "\n",
     "d['sample'] = dict(\n",
     "    sample_name=sample_name,\n",
-    "    dye_names=[n.encode() for n in dye_names],\n",
+    "    dye_names=dye_names,\n",
     "    buffer_name=buffer_name,\n",
-    "    num_dyes = len(dye_names))\n",
+    "    num_dyes = len(dye_names.split(',')))\n",
     "\n",
     "d['identity'] = dict(\n",
     "    author=author,\n",

diff --git a/notebooks/Convert ns-ALEX HT3 files to Photon-HDF5.ipynb b/notebooks/Convert ns-ALEX HT3 files to Photon-HDF5.ipynb
@@ -133,7 +133,7 @@
    "source": [
     "description = 'A demostrative smFRET-nsALEX measurement.'\n",
     "sample_name = 'Doubly-labeled ssDNA partially hybridized to a complementary strand.'\n",
-    "dye_names = ['ATTO488', 'ATTO647N']\n",
+    "dye_names = 'ATTO488, ATTO647N'\n",
     "buffer_name = 'Tris20 mM Ph 7.8'"
    ]
   },
@@ -281,9 +281,9 @@
     "\n",
     "d['sample'] = dict(\n",
     "    sample_name=sample_name,\n",
-    "    dye_names=[n.encode() for n in dye_names],\n",
+    "    dye_names=dye_names,\n",
     "    buffer_name=buffer_name,\n",
-    "    num_dyes = len(dye_names))\n",
+    "    num_dyes = len(dye_names.split(',')))\n",
     "\n",
     "d['identity'] = dict(\n",
     "    author=author,\n",
@@ -531,21 +531,21 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 2",
    "language": "python",
-   "name": "python3"
+   "name": "python2"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 3
+    "version": 2
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.4.3"
+   "pygments_lexer": "ipython2",
+   "version": "2.7.9"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/Convert us-ALEX SM files to Photon-HDF5.ipynb b/notebooks/Convert us-ALEX SM files to Photon-HDF5.ipynb
@@ -133,7 +133,7 @@
    "source": [
     "description = 'A demostrative smFRET-usALEX measurement.'\n",
     "sample_name = '022rde11_T_minus15_acc__NT_plus10_don_1'\n",
-    "dye_names = ['ATTO550', 'ATTO647N']\n",
+    "dye_names = 'ATTO550, ATTO647N'\n",
     "buffer_name = 'Transcription buffer.'"
    ]
   },
@@ -281,9 +281,9 @@
     "\n",
     "d['sample'] = dict(\n",
     "    sample_name=sample_name,\n",
-    "    dye_names=[n.encode() for n in dye_names],\n",
+    "    dye_names=dye_names,\n",
     "    buffer_name=buffer_name,\n",
-    "    num_dyes = len(dye_names))\n",
+    "    num_dyes = len(dye_names.split(',')))\n",
     "\n",
     "d['identity'] = dict(\n",
     "    author=author,\n",
@@ -441,21 +441,21 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 2",
    "language": "python",
-   "name": "python3"
+   "name": "python2"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 3
+    "version": 2
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.4.3"
+   "pygments_lexer": "ipython2",
+   "version": "2.7.9"
   }
  },
  "nbformat": 4,

diff --git a/phconvert/specs/photon-hdf5_specs.json b/phconvert/specs/photon-hdf5_specs.json
@@ -288,8 +288,8 @@
         "scalar"
     ],
     "/sample/dye_names": [
-        "List of dye names present in the sample.",
-        "array"
+        "String containing a comma-separated list of dye or fluorophore names.",
+        "string"
     ],
     "/sample/buffer_name": [
         "A descriptive name for the buffer.",